DOI: 10.1126/science.273.5282.1678. Crystal Structure of a Group I Ribozyme Domain: Principles of RNA Packing

Crystal Structure of a Group I Ribozyme Domain: Principles of RNA Packing

10.1126/science.273.5282.1678

Crossref journal-article

American Association for the Advancement of Science (AAAS)

Science (221)

Abstract

Group I self-splicing introns catalyze their own excision from precursor RNAs by way of a two-step transesterification reaction. The catalytic core of these ribozymes is formed by two structural domains. The 2.8-angstrom crystal structure of one of these, the P4-P6 domain of the Tetrahymena thermophila intron, is described. In the 160-nucleotide domain, a sharp bend allows stacked helices of the conserved core to pack alongside helices of an adjacent region. Two specific long-range interactions clamp the two halves of the domain together: a two-Mg 2+ -coordinated adenosine-rich corkscrew plugs into the minor groove of a helix, and a GAAA hairpin loop binds to a conserved 11-nucleotide internal loop. Metal- and ribose-mediated backbone contacts further stabilize the close side-by-side helical packing. The structure indicates the extent of RNA packing required for the function of large ribozymes, the spliceosome, and the ribosome.

Bibliography

Cate, J. H., Gooding, A. R., Podell, E., Zhou, K., Golden, B. L., Kundrot, C. E., Cech, T. R., & Doudna, J. A. (1996). Crystal Structure of a Group I Ribozyme Domain: Principles of RNA Packing. Science, 273(5282), 1678â1685.

Authors 8

Jamie H. Cate (first)
Anne R. Gooding (additional)
Elaine Podell (additional)
Kaihong Zhou (additional)
Barbara L. Golden (additional)
Craig E. Kundrot (additional)
Thomas R. Cech (additional)
Jennifer A. Doudna (additional)

References 76 Referenced 903

Cech T. R., Annu. Rev. Biochem. 59, 543 (1990). (10.1146/annurev.bi.59.070190.002551) / Annu. Rev. Biochem. by Cech T. R. (1990)
Saldanha R., Mohr G., Belfort M., Lambowitz A. M., FASEB J. 7, 15 (1993). (10.1096/fasebj.7.1.8422962) / FASEB J. by Saldanha R. (1993)
10.1126/science.2501870
Celander D. W., Cech T. R., Biochemistry 29, 1355 (1990). (10.1021/bi00458a001) / Biochemistry by Celander D. W. (1990)
10.1126/science.1989074
Grosshans C. A., Cech T. R., Biochemistry 28, 6888 (1989). (10.1021/bi00443a017) / Biochemistry by Grosshans C. A. (1989)
Piccirilli J. A., Vyle J. S., Caruthers M. H., Cech T. R., Nature 361, 85 (1993). (10.1038/361085a0) / Nature by Piccirilli J. A. (1993)
Christian E. L., Yarus M., Biochemistry 32, 4475 (1993). (10.1021/bi00068a001) / Biochemistry by Christian E. L. (1993)
Michel F., Westhof E., J. Mol. Biol. 216, 585 (1990). (10.1016/0022-2836(90)90386-Z) / J. Mol. Biol. by Michel F. (1990)
Murphy F. L., Cech T. R., ibid. 236, 49 (1994). / ibid. by Murphy F. L. (1994)
Laggerbauer B., Murphy F. L., Cech T. R., EMBO J. 13, 2669 (1994). (10.1002/j.1460-2075.1994.tb06557.x) / EMBO J. by Laggerbauer B. (1994)
Wang Y. H., Murphy F. L., Cech T. R., Griffith J. D., J. Mol. Biol. 236, 64 (1994). (10.1006/jmbi.1994.1118) / J. Mol. Biol. by Wang Y. H. (1994)
Doudna J. A., Cech T. R., RNA 1, 36 (1995). / RNA by Doudna J. A. (1995)
10.1126/science.8052848
Downs W. and , Cech T. R., RNA 2, 718 (1996). / RNA by Downs W. (1996)
Michel F., Dujon B., EMBO J. 2, 33 (1983). (10.1002/j.1460-2075.1983.tb01376.x) / EMBO J. by Michel F. (1983)
Burke J. M., et al., Nucleic Acids Res. 15, 7217 (1987). (10.1093/nar/15.18.7217) / Nucleic Acids Res. by Burke J. M. (1987)
Cech T., Damberger S., Gutell R., Nature Struct. Biol. 1, 273 (1994). (10.1038/nsb0594-273) / Nature Struct. Biol. by Cech T. (1994)
Collins R. A., Nucleic Acids Res. 16, 2705 (1988). (10.1093/nar/16.6.2705) / Nucleic Acids Res. by Collins R. A. (1988)
Mohr G., Caprara M. G., Guo Q., Lambowitz A. M., Nature 370, 147 (1994). (10.1038/370147a0) / Nature by Mohr G. (1994)
Joyce G. F., van der Horst G., Inoue T., Nucleic Acids Res. 17, 7879 (1989). (10.1093/nar/17.19.7879) / Nucleic Acids Res. by Joyce G. F. (1989)
van der Horst G., Christian A., Inoue T., Proc. Natl. Acad. Sci. U.S.A. 88, 184 (1991). (10.1073/pnas.88.1.184) / Proc. Natl. Acad. Sci. U.S.A. by van der Horst G. (1991)
10.1126/science.179.4070.285
Robertus J. D., et al., Nature 250, 546 (1974). (10.1038/250546a0) / Nature by Robertus J. D. (1974)
Schevitz R. W., Podjarny A. D., Krishnamachari N., Hughes J. J., Sigler P. B., ibid. 278, 188 (1979). / ibid. by Schevitz R. W. (1979)
Moras D., et al., ibid. 288, 669 (1980). / ibid. by Moras D. (1980)
Woo N. H., Roe B. A., Rich A., ibid. 286, 346 (1980). / ibid. by Woo N. H. (1980)
Pley H. W., Flaherty K. M., McKay D. B., ibid. 372, 68 (1994). / ibid. by Pley H. W. (1994)
Scott W. G., Finch J. T., Klug A., Cell 81, 995 (1995). / Cell by Scott W. G. (1995)
Reviewed by J. R. Wyatt and I. Tinoco Jr. in The RNA World R. F. Gesteland and J. F. Atkins Eds. (Cold Spring Harbor Laboratory Press Cold Spring Harbor NY 1993) p. 465
L. X. Shen Z. Cai I. Tinoco Jr. FASEB J. 9 1023 (1995). (10.1096/fasebj.9.11.7544309)
Doudna J. A., Grosshans C., Gooding A., Kundrot C. E., Proc. Natl. Acad. Sci. U.S.A. 90, 7829 (1993). (10.1073/pnas.90.16.7829) / Proc. Natl. Acad. Sci. U.S.A. by Doudna J. A. (1993)
Lay P. A., Magnuson R. H., Taube H., Inorg. Chem. 28, 3001 (1989). (10.1021/ic00314a026) / Inorg. Chem. by Lay P. A. (1989)
Golden B. L. Gooding A. R. Podell E. Cech T. R. in preparation.
Both molecules A and B contain residues 103 through 260. In the crystals ∼50 percent of the RNA is nicked in loop L6b between residues C237 and U238 [determined by direct RNA sequencing and primer extension analysis of RNA in crystals (unpublished data)]. For both molecules L6b has fairly continuous density in the experimental map for the backbone; the bases for nucleotides 236 through 239 have not been modeled. In each molecule there are three to four residues where the phosphate density is visible in the map but the base or ribose and base are not. In these cases the full nucleotide has been included for refinement but the occupancy for the missing component has been set to zero.
Cate J. H., Doudna J. A., Structurein press. / Structure by Cate J. H.
Kallenbach N. E., Berman H. M., Q. Rev. Biophys. 10, 138 (1977). (10.1017/S0033583500000202) / Q. Rev. Biophys. by Kallenbach N. E. (1977)
Murphy F. L., Cech T. R., Biochemistry 32, 5291 (1993). (10.1021/bi00071a003) / Biochemistry by Murphy F. L. (1993)
Flor P. J., Flanegan J. B., Cech T. R., EMBO J. 8, 3391 (1989). (10.1002/j.1460-2075.1989.tb08503.x) / EMBO J. by Flor P. J. (1989)
10.1073/pnas.87.21.8467
10.1002/j.1460-2075.1995.tb07111.x
10.1126/science.1712983
10.1038/372111a0
10.1126/science.273.5282.1696
Bartel D. P., Zapp M. L., Green M. R., Szostak J. W., Cell 67, 529 (1991). (10.1016/0092-8674(91)90527-6) / Cell by Bartel D. P. (1991)
Peterson R. D., Bartel D. P., Szostak J. W., Horvath S. J., Feigon J., Biochemistry 33, 5357 (1994). (10.1021/bi00184a001) / Biochemistry by Peterson R. D. (1994)
Battiste J. L., Tan R., Frankel A. D., Williamson J. R., ibid.: 2741. / ibid. by Battiste J. L.
Free radicals produced by Fe(II)-EDTA in solution (presumably ·OH) cleave RNA without substantial specificity for base sequence or single- or double-strandedness and therefore are useful for probing the solvent accessibility of elements within complex folded RNAs (3 4 5).
Intermolecular hydrogen bonds between O2′ atoms of duplex RNAs in a crystal have also been reported by H. Schindelin et al. J. Mol. Biol. 249 595 (1995).
Guerrier-Takada C., Haydock K., Allen L., Altman S., Biochemistry 25, 1509 (1986). (10.1021/bi00355a006) / Biochemistry by Guerrier-Takada C. (1986)
Smith D., Burgin A. B., Haas E. S., Pace N. R., J. Biol. Chem. 267, 2429 (1992); (10.1016/S0021-9258(18)45897-8) / J. Biol. Chem. by Smith D. (1992)
Smith D. and , Pace N. R., Biochemistry 32, 5273 (1993). (10.1021/bi00071a001) / Biochemistry by Smith D. (1993)
10.1126/science.7688142
Jack A., Ladner J. E., Rhodes D., Brown R. S., Klug A., J. Mol. Biol. 111, 315 (1977); (10.1016/S0022-2836(77)80054-5) / J. Mol. Biol. by Jack A. (1977)
Holbrook S. R., Sussman J. L., Warrant R. W., Church G. M., Kim S. H., Nucleic Acids Res. 4, 2811 (1977). (10.1093/nar/4.8.2811) / Nucleic Acids Res. by Holbrook S. R. (1977)
Cate J. H. Doudna J. A. in preparation.
The two molecules (A and B) in the asymmetric unit of the crystal show different degrees of order at the 5′ end. In molecule B clear density is seen in the solvent-flattened experimental map for all but the first G of the sequence; in molecule A the density is weak for the first 4 nt of the sequence.
Michel F., Ellington A. D., Couture S., Szostak J. W., Nature 347, 578 (1990). (10.1038/347578a0) / Nature by Michel F. (1990)
10.1126/science.7682726
Michel F., Hanna M., Green R., Bartel D. P., Szostak J. W., Nature 342, 391 (1989). (10.1038/342391a0) / Nature by Michel F. (1989)
10.1126/science.1315076
10.1038/358123a0
Strobel S. A., Cech T. R., Biochemistry 35, 1201 (1996). (10.1021/bi952244f) / Biochemistry by Strobel S. A. (1996)
10.1016/0022-2836(68)90392-6
Cech T. R., Gene 135, 33 (1993). (10.1016/0378-1119(93)90046-6) / Gene by Cech T. R. (1993)
Cuenoud B., Szostak J. W., Nature 375, 611 (1995); (10.1038/375611a0) / Nature by Cuenoud B. (1995)
Breaker R. R. and , Joyce G. F., Chem. Biol. 1, 223 (1994); (10.1016/1074-5521(94)90014-0) / Chem. Biol. by Breaker R. R. (1994)
ibid. 2, 655 (1995). / ibid. (1995)
Otwinowski Z., in Isomorphous Replacement and Anomalous Scattering, , Wolf W., Evans P. R., Leslie A. G. W., Eds. (SERC Daresbury Laboratory, Warington, UK, 1991), pp. 80-86. / Isomorphous Replacement and Anomalous Scattering by Otwinowski Z. (1991)
Acta Crystallogr. D vol. 50 (1994) p. 760Collaborative Computing Project Number 4. (10.1107/S0907444994003112)
10.1107/S0108767390010224
Brünger A., X-PLOR Manual, Version 3.1: A System for X-ray Crystallography and NMR (Yale Univ. Press, New Haven, CT, 1993). / X-PLOR Manual, Version 3.1: A System for X-ray Crystallography and NMR by Brünger A. (1993)
Carson M., J. Appl. Cryst. 24, 958 (1991). (10.1107/S0021889891007240) / J. Appl. Cryst. by Carson M. (1991)
10.1126/science.8085157
The MidasPlus program was developed at the Computer Graphics Laboratory University of California San Francisco (supported by NIH RR-01081).
We thank H. Taube of Stanford University for the osmium hexammine triflate; T. Steitz S. Schultz A. Brünger A. Ferré-d'Amaré C. Correll D. Engelman A. Friedman T. Griffin J. Jaeger A. M. Pyle V. Rath L. Rice L. Silvian S. Strobel J. Wang and members of the Center for Structural Biology at Yale for many helpful discussions; V. Carperos L. Doherty A. Ferré-d'Amaré C. Correll and J. Jaeger for help with data collection; V. Rath and Pfizer Inc. of Groton CT for use of data collection equipment; C. Ogata and W. Hendrickson for useful discussions and data collection time at beamline X-4A at the National Synchrotron Light Source Brookhaven National Laboratory Upton NY; the staff at Cornell High Energy Synchrotron Source (CHESS) beamline A-1; A. Thompson and the staff at beamline BL-19 at the European Synchrotron Radiation Facility (ESRF) Grenoble France; and A. Ferré-d'Amaré V. Rath and S. Strobel for review of the manuscript. Supported by the Lucille P. Markey Charitable Trust Scholars Program the Donaghue Medical Research Foundation NIH grant GM22778-21 the Searle Scholars Program and the Beckman Young Investigators Program (J.A.D.) NIH training grant 5T32GM08283-07 (J.H.C.) American Cancer Society postdoctoral fellowship (B.L.G.) NSF grant MCB-9221307 (C.E.K.) Howard Hughes Medical Institute (T.R.C.) and the Keck Foundation (C.E.K. and T.R.C.).

Dates

Type	When
Created	18 years, 9 months ago (Oct. 27, 2006, 2:30 p.m.)
Deposited	1 year ago (Aug. 7, 2024, 7:42 a.m.)
Indexed	5 days, 8 hours ago (Aug. 19, 2025, 6:34 a.m.)
Issued	28 years, 11 months ago (Sept. 20, 1996)
Published	28 years, 11 months ago (Sept. 20, 1996)
Published Print	28 years, 11 months ago (Sept. 20, 1996)

Funders 0

None

BibTeX

@article{Cate_1996, title={Crystal Structure of a Group I Ribozyme Domain: Principles of RNA Packing}, volume={273}, ISSN={1095-9203}, url={http://dx.doi.org/10.1126/science.273.5282.1678}, DOI={10.1126/science.273.5282.1678}, number={5282}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Cate, Jamie H. and Gooding, Anne R. and Podell, Elaine and Zhou, Kaihong and Golden, Barbara L. and Kundrot, Craig E. and Cech, Thomas R. and Doudna, Jennifer A.}, year={1996}, month=sep, pages={1678–1685} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        8,
        19
      ]
    ],
    "date-time": "2025-08-19T10:34:07Z",
    "timestamp": 1755599647126
  },
  "reference-count": 76,
  "publisher": "American Association for the Advancement of Science (AAAS)",
  "issue": "5282",
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        1996,
        9,
        20
      ]
    ]
  },
  "abstract": "<jats:p>\n            Group I self-splicing introns catalyze their own excision from precursor RNAs by way of a two-step transesterification reaction. The catalytic core of these ribozymes is formed by two structural domains. The 2.8-angstrom crystal structure of one of these, the P4-P6 domain of the\n            <jats:italic>Tetrahymena thermophila</jats:italic>\n            intron, is described. In the 160-nucleotide domain, a sharp bend allows stacked helices of the conserved core to pack alongside helices of an adjacent region. Two specific long-range interactions clamp the two halves of the domain together: a two-Mg\n            <jats:sup>2+</jats:sup>\n            -coordinated adenosine-rich corkscrew plugs into the minor groove of a helix, and a GAAA hairpin loop binds to a conserved 11-nucleotide internal loop. Metal- and ribose-mediated backbone contacts further stabilize the close side-by-side helical packing. The structure indicates the extent of RNA packing required for the function of large ribozymes, the spliceosome, and the ribosome.\n          </jats:p>",
  "DOI": "10.1126/science.273.5282.1678",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2006,
        10,
        27
      ]
    ],
    "date-time": "2006-10-27T18:30:41Z",
    "timestamp": 1161973841000
  },
  "page": "1678-1685",
  "source": "Crossref",
  "is-referenced-by-count": 903,
  "title": "Crystal Structure of a Group I Ribozyme Domain: Principles of RNA Packing",
  "prefix": "10.1126",
  "volume": "273",
  "author": [
    {
      "given": "Jamie H.",
      "family": "Cate",
      "sequence": "first",
      "affiliation": [
        {
          "name": "J. H. Cate, K. Zhou, and J. A. Doudna are in the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA;"
        }
      ]
    },
    {
      "given": "Anne R.",
      "family": "Gooding",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "A. R. Gooding, E. Podell, B. L. Golden, C. E. Kundrot, and T. R. Cech are in the Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA;"
        },
        {
          "name": "A. R. Gooding, B. L. Golden, E. Podell, and T. Cech are also with the Howard Hughes Medical Institute at Boulder, CO 80309, USA."
        }
      ]
    },
    {
      "given": "Elaine",
      "family": "Podell",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "A. R. Gooding, E. Podell, B. L. Golden, C. E. Kundrot, and T. R. Cech are in the Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA;"
        },
        {
          "name": "A. R. Gooding, B. L. Golden, E. Podell, and T. Cech are also with the Howard Hughes Medical Institute at Boulder, CO 80309, USA."
        }
      ]
    },
    {
      "given": "Kaihong",
      "family": "Zhou",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "J. H. Cate, K. Zhou, and J. A. Doudna are in the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA;"
        }
      ]
    },
    {
      "given": "Barbara L.",
      "family": "Golden",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "A. R. Gooding, E. Podell, B. L. Golden, C. E. Kundrot, and T. R. Cech are in the Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA;"
        },
        {
          "name": "A. R. Gooding, B. L. Golden, E. Podell, and T. Cech are also with the Howard Hughes Medical Institute at Boulder, CO 80309, USA."
        }
      ]
    },
    {
      "given": "Craig E.",
      "family": "Kundrot",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "A. R. Gooding, E. Podell, B. L. Golden, C. E. Kundrot, and T. R. Cech are in the Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA;"
        }
      ]
    },
    {
      "given": "Thomas R.",
      "family": "Cech",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "A. R. Gooding, E. Podell, B. L. Golden, C. E. Kundrot, and T. R. Cech are in the Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA;"
        },
        {
          "name": "A. R. Gooding, B. L. Golden, E. Podell, and T. Cech are also with the Howard Hughes Medical Institute at Boulder, CO 80309, USA."
        }
      ]
    },
    {
      "given": "Jennifer A.",
      "family": "Doudna",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "J. H. Cate, K. Zhou, and J. A. Doudna are in the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA;"
        }
      ]
    }
  ],
  "member": "221",
  "reference": [
    {
      "key": "e_1_3_1_2_2",
      "doi-asserted-by": "crossref",
      "first-page": "543",
      "DOI": "10.1146/annurev.bi.59.070190.002551",
      "volume": "59",
      "author": "Cech T. R.",
      "year": "1990",
      "unstructured": "Cech T. R., Annu. Rev. Biochem. 59, 543 (1990).",
      "journal-title": "Annu. Rev. Biochem."
    },
    {
      "key": "e_1_3_1_3_2",
      "doi-asserted-by": "crossref",
      "first-page": "15",
      "DOI": "10.1096/fasebj.7.1.8422962",
      "volume": "7",
      "author": "Saldanha R.",
      "year": "1993",
      "unstructured": "Saldanha R., Mohr G., Belfort M., Lambowitz A. M., FASEB J. 7, 15 (1993).",
      "journal-title": "FASEB J."
    },
    {
      "key": "e_1_3_1_4_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.2501870"
    },
    {
      "key": "e_1_3_1_5_2",
      "doi-asserted-by": "crossref",
      "first-page": "1355",
      "DOI": "10.1021/bi00458a001",
      "volume": "29",
      "author": "Celander D. W.",
      "year": "1990",
      "unstructured": "Celander D. W., Cech T. R., Biochemistry 29, 1355 (1990).",
      "journal-title": "Biochemistry"
    },
    {
      "key": "e_1_3_1_6_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.1989074"
    },
    {
      "key": "e_1_3_1_7_2",
      "doi-asserted-by": "crossref",
      "first-page": "6888",
      "DOI": "10.1021/bi00443a017",
      "volume": "28",
      "author": "Grosshans C. A.",
      "year": "1989",
      "unstructured": "Grosshans C. A., Cech T. R., Biochemistry 28, 6888 (1989).",
      "journal-title": "Biochemistry"
    },
    {
      "key": "e_1_3_1_8_2",
      "doi-asserted-by": "crossref",
      "first-page": "85",
      "DOI": "10.1038/361085a0",
      "volume": "361",
      "author": "Piccirilli J. A.",
      "year": "1993",
      "unstructured": "Piccirilli J. A., Vyle J. S., Caruthers M. H., Cech T. R., Nature 361, 85 (1993).",
      "journal-title": "Nature"
    },
    {
      "key": "e_1_3_1_9_2",
      "doi-asserted-by": "crossref",
      "first-page": "4475",
      "DOI": "10.1021/bi00068a001",
      "volume": "32",
      "author": "Christian E. L.",
      "year": "1993",
      "unstructured": "Christian E. L., Yarus M., Biochemistry 32, 4475 (1993).",
      "journal-title": "Biochemistry"
    },
    {
      "key": "e_1_3_1_10_2",
      "doi-asserted-by": "crossref",
      "first-page": "585",
      "DOI": "10.1016/0022-2836(90)90386-Z",
      "volume": "216",
      "author": "Michel F.",
      "year": "1990",
      "unstructured": "Michel F., Westhof E., J. Mol. Biol. 216, 585 (1990).",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "e_1_3_1_11_2",
      "first-page": "49",
      "volume": "236",
      "author": "Murphy F. L.",
      "year": "1994",
      "unstructured": "Murphy F. L., Cech T. R., ibid. 236, 49 (1994).",
      "journal-title": "ibid."
    },
    {
      "key": "e_1_3_1_12_2",
      "doi-asserted-by": "crossref",
      "first-page": "2669",
      "DOI": "10.1002/j.1460-2075.1994.tb06557.x",
      "volume": "13",
      "author": "Laggerbauer B.",
      "year": "1994",
      "unstructured": "Laggerbauer B., Murphy F. L., Cech T. R., EMBO J. 13, 2669 (1994).",
      "journal-title": "EMBO J."
    },
    {
      "key": "e_1_3_1_13_2",
      "doi-asserted-by": "crossref",
      "first-page": "64",
      "DOI": "10.1006/jmbi.1994.1118",
      "volume": "236",
      "author": "Wang Y. H.",
      "year": "1994",
      "unstructured": "Wang Y. H., Murphy F. L., Cech T. R., Griffith J. D., J. Mol. Biol. 236, 64 (1994).",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "e_1_3_1_14_2",
      "first-page": "36",
      "volume": "1",
      "author": "Doudna J. A.",
      "year": "1995",
      "unstructured": "Doudna J. A., Cech T. R., RNA 1, 36 (1995).",
      "journal-title": "RNA"
    },
    {
      "key": "e_1_3_1_15_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.8052848"
    },
    {
      "key": "e_1_3_1_15_3",
      "first-page": "718",
      "volume": "2",
      "author": "Downs W.",
      "year": "1996",
      "unstructured": "Downs W. and , Cech T. R., RNA 2, 718 (1996).",
      "journal-title": "RNA"
    },
    {
      "key": "e_1_3_1_16_2",
      "doi-asserted-by": "crossref",
      "first-page": "33",
      "DOI": "10.1002/j.1460-2075.1983.tb01376.x",
      "volume": "2",
      "author": "Michel F.",
      "year": "1983",
      "unstructured": "Michel F., Dujon B., EMBO J. 2, 33 (1983).",
      "journal-title": "EMBO J."
    },
    {
      "key": "e_1_3_1_17_2",
      "doi-asserted-by": "crossref",
      "first-page": "7217",
      "DOI": "10.1093/nar/15.18.7217",
      "volume": "15",
      "author": "Burke J. M.",
      "year": "1987",
      "unstructured": "Burke J. M., et al., Nucleic Acids Res. 15, 7217 (1987).",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "e_1_3_1_18_2",
      "doi-asserted-by": "crossref",
      "first-page": "273",
      "DOI": "10.1038/nsb0594-273",
      "volume": "1",
      "author": "Cech T.",
      "year": "1994",
      "unstructured": "Cech T., Damberger S., Gutell R., Nature Struct. Biol. 1, 273 (1994).",
      "journal-title": "Nature Struct. Biol."
    },
    {
      "key": "e_1_3_1_19_2",
      "doi-asserted-by": "crossref",
      "first-page": "2705",
      "DOI": "10.1093/nar/16.6.2705",
      "volume": "16",
      "author": "Collins R. A.",
      "year": "1988",
      "unstructured": "Collins R. A., Nucleic Acids Res. 16, 2705 (1988).",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "e_1_3_1_20_2",
      "doi-asserted-by": "crossref",
      "first-page": "147",
      "DOI": "10.1038/370147a0",
      "volume": "370",
      "author": "Mohr G.",
      "year": "1994",
      "unstructured": "Mohr G., Caprara M. G., Guo Q., Lambowitz A. M., Nature 370, 147 (1994).",
      "journal-title": "Nature"
    },
    {
      "key": "e_1_3_1_21_2",
      "doi-asserted-by": "crossref",
      "first-page": "7879",
      "DOI": "10.1093/nar/17.19.7879",
      "volume": "17",
      "author": "Joyce G. F.",
      "year": "1989",
      "unstructured": "Joyce G. F., van der Horst G., Inoue T., Nucleic Acids Res. 17, 7879 (1989).",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "e_1_3_1_22_2",
      "doi-asserted-by": "crossref",
      "first-page": "184",
      "DOI": "10.1073/pnas.88.1.184",
      "volume": "88",
      "author": "van der Horst G.",
      "year": "1991",
      "unstructured": "van der Horst G., Christian A., Inoue T., Proc. Natl. Acad. Sci. U.S.A. 88, 184 (1991).",
      "journal-title": "Proc. Natl. Acad. Sci. U.S.A."
    },
    {
      "key": "e_1_3_1_23_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.179.4070.285"
    },
    {
      "key": "e_1_3_1_24_2",
      "doi-asserted-by": "crossref",
      "first-page": "546",
      "DOI": "10.1038/250546a0",
      "volume": "250",
      "author": "Robertus J. D.",
      "year": "1974",
      "unstructured": "Robertus J. D., et al., Nature 250, 546 (1974).",
      "journal-title": "Nature"
    },
    {
      "key": "e_1_3_1_25_2",
      "first-page": "188",
      "volume": "278",
      "author": "Schevitz R. W.",
      "year": "1979",
      "unstructured": "Schevitz R. W., Podjarny A. D., Krishnamachari N., Hughes J. J., Sigler P. B., ibid. 278, 188 (1979).",
      "journal-title": "ibid."
    },
    {
      "key": "e_1_3_1_26_2",
      "first-page": "669",
      "volume": "288",
      "author": "Moras D.",
      "year": "1980",
      "unstructured": "Moras D., et al., ibid. 288, 669 (1980).",
      "journal-title": "ibid."
    },
    {
      "key": "e_1_3_1_27_2",
      "first-page": "346",
      "volume": "286",
      "author": "Woo N. H.",
      "year": "1980",
      "unstructured": "Woo N. H., Roe B. A., Rich A., ibid. 286, 346 (1980).",
      "journal-title": "ibid."
    },
    {
      "key": "e_1_3_1_28_2",
      "first-page": "68",
      "volume": "372",
      "author": "Pley H. W.",
      "year": "1994",
      "unstructured": "Pley H. W., Flaherty K. M., McKay D. B., ibid. 372, 68 (1994).",
      "journal-title": "ibid."
    },
    {
      "key": "e_1_3_1_29_2",
      "first-page": "995",
      "volume": "81",
      "author": "Scott W. G.",
      "year": "1995",
      "unstructured": "Scott W. G., Finch J. T., Klug A., Cell 81, 995 (1995).",
      "journal-title": "Cell"
    },
    {
      "key": "#cr-split#-e_1_3_1_30_2.1",
      "unstructured": "Reviewed by J. R. Wyatt and I. Tinoco Jr. in The RNA World R. F. Gesteland and J. F. Atkins Eds. (Cold Spring Harbor Laboratory Press Cold Spring Harbor NY 1993) p. 465"
    },
    {
      "key": "#cr-split#-e_1_3_1_30_2.2",
      "doi-asserted-by": "crossref",
      "unstructured": "L. X. Shen Z. Cai I. Tinoco Jr. FASEB J. 9 1023 (1995).",
      "DOI": "10.1096/fasebj.9.11.7544309"
    },
    {
      "key": "e_1_3_1_31_2",
      "doi-asserted-by": "crossref",
      "first-page": "7829",
      "DOI": "10.1073/pnas.90.16.7829",
      "volume": "90",
      "author": "Doudna J. A.",
      "year": "1993",
      "unstructured": "Doudna J. A., Grosshans C., Gooding A., Kundrot C. E., Proc. Natl. Acad. Sci. U.S.A. 90, 7829 (1993).",
      "journal-title": "Proc. Natl. Acad. Sci. U.S.A."
    },
    {
      "key": "e_1_3_1_32_2",
      "doi-asserted-by": "crossref",
      "first-page": "3001",
      "DOI": "10.1021/ic00314a026",
      "volume": "28",
      "author": "Lay P. A.",
      "year": "1989",
      "unstructured": "Lay P. A., Magnuson R. H., Taube H., Inorg. Chem. 28, 3001 (1989).",
      "journal-title": "Inorg. Chem."
    },
    {
      "key": "e_1_3_1_33_2",
      "unstructured": "Golden B. L. Gooding A. R. Podell E. Cech T. R. in preparation."
    },
    {
      "key": "e_1_3_1_34_2",
      "unstructured": "Both molecules A and B contain residues 103 through 260. In the crystals \u223c50 percent of the RNA is nicked in loop L6b between residues C237 and U238 [determined by direct RNA sequencing and primer extension analysis of RNA in crystals (unpublished data)]. For both molecules L6b has fairly continuous density in the experimental map for the backbone; the bases for nucleotides 236 through 239 have not been modeled. In each molecule there are three to four residues where the phosphate density is visible in the map but the base or ribose and base are not. In these cases the full nucleotide has been included for refinement but the occupancy for the missing component has been set to zero."
    },
    {
      "journal-title": "Structure",
      "author": "Cate J. H.",
      "key": "e_1_3_1_35_2",
      "unstructured": "Cate J. H., Doudna J. A., Structurein press."
    },
    {
      "key": "e_1_3_1_36_2",
      "doi-asserted-by": "crossref",
      "first-page": "138",
      "DOI": "10.1017/S0033583500000202",
      "volume": "10",
      "author": "Kallenbach N. E.",
      "year": "1977",
      "unstructured": "Kallenbach N. E., Berman H. M., Q. Rev. Biophys. 10, 138 (1977).",
      "journal-title": "Q. Rev. Biophys."
    },
    {
      "key": "e_1_3_1_37_2",
      "doi-asserted-by": "crossref",
      "first-page": "5291",
      "DOI": "10.1021/bi00071a003",
      "volume": "32",
      "author": "Murphy F. L.",
      "year": "1993",
      "unstructured": "Murphy F. L., Cech T. R., Biochemistry 32, 5291 (1993).",
      "journal-title": "Biochemistry"
    },
    {
      "key": "e_1_3_1_38_2",
      "doi-asserted-by": "crossref",
      "first-page": "3391",
      "DOI": "10.1002/j.1460-2075.1989.tb08503.x",
      "volume": "8",
      "author": "Flor P. J.",
      "year": "1989",
      "unstructured": "Flor P. J., Flanegan J. B., Cech T. R., EMBO J. 8, 3391 (1989).",
      "journal-title": "EMBO J."
    },
    {
      "key": "e_1_3_1_39_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.87.21.8467"
    },
    {
      "key": "e_1_3_1_40_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/j.1460-2075.1995.tb07111.x"
    },
    {
      "key": "e_1_3_1_41_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.1712983"
    },
    {
      "key": "e_1_3_1_42_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/372111a0"
    },
    {
      "key": "e_1_3_1_43_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.273.5282.1696"
    },
    {
      "key": "e_1_3_1_44_2",
      "doi-asserted-by": "crossref",
      "first-page": "529",
      "DOI": "10.1016/0092-8674(91)90527-6",
      "volume": "67",
      "author": "Bartel D. P.",
      "year": "1991",
      "unstructured": "Bartel D. P., Zapp M. L., Green M. R., Szostak J. W., Cell 67, 529 (1991).",
      "journal-title": "Cell"
    },
    {
      "key": "e_1_3_1_45_2",
      "doi-asserted-by": "crossref",
      "first-page": "5357",
      "DOI": "10.1021/bi00184a001",
      "volume": "33",
      "author": "Peterson R. D.",
      "year": "1994",
      "unstructured": "Peterson R. D., Bartel D. P., Szostak J. W., Horvath S. J., Feigon J., Biochemistry 33, 5357 (1994).",
      "journal-title": "Biochemistry"
    },
    {
      "key": "e_1_3_1_46_2",
      "first-page": "2741",
      "author": "Battiste J. L.",
      "unstructured": "Battiste J. L., Tan R., Frankel A. D., Williamson J. R., ibid.: 2741.",
      "journal-title": "ibid."
    },
    {
      "key": "e_1_3_1_47_2",
      "unstructured": "Free radicals produced by Fe(II)-EDTA in solution (presumably \u00b7OH) cleave RNA without substantial specificity for base sequence or single- or double-strandedness and therefore are useful for probing the solvent accessibility of elements within complex folded RNAs (3 4 5)."
    },
    {
      "key": "e_1_3_1_48_2",
      "unstructured": "Intermolecular hydrogen bonds between O2\u2032 atoms of duplex RNAs in a crystal have also been reported by H. Schindelin et al. J. Mol. Biol. 249 595 (1995)."
    },
    {
      "key": "e_1_3_1_49_2",
      "doi-asserted-by": "crossref",
      "first-page": "1509",
      "DOI": "10.1021/bi00355a006",
      "volume": "25",
      "author": "Guerrier-Takada C.",
      "year": "1986",
      "unstructured": "Guerrier-Takada C., Haydock K., Allen L., Altman S., Biochemistry 25, 1509 (1986).",
      "journal-title": "Biochemistry"
    },
    {
      "key": "e_1_3_1_50_2",
      "doi-asserted-by": "crossref",
      "first-page": "2429",
      "DOI": "10.1016/S0021-9258(18)45897-8",
      "volume": "267",
      "author": "Smith D.",
      "year": "1992",
      "unstructured": "Smith D., Burgin A. B., Haas E. S., Pace N. R., J. Biol. Chem. 267, 2429 (1992);",
      "journal-title": "J. Biol. Chem."
    },
    {
      "key": "e_1_3_1_50_3",
      "doi-asserted-by": "crossref",
      "first-page": "5273",
      "DOI": "10.1021/bi00071a001",
      "volume": "32",
      "author": "Smith D.",
      "year": "1993",
      "unstructured": "Smith D. and , Pace N. R., Biochemistry 32, 5273 (1993).",
      "journal-title": "Biochemistry"
    },
    {
      "key": "e_1_3_1_51_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.7688142"
    },
    {
      "key": "e_1_3_1_52_2",
      "doi-asserted-by": "crossref",
      "first-page": "315",
      "DOI": "10.1016/S0022-2836(77)80054-5",
      "volume": "111",
      "author": "Jack A.",
      "year": "1977",
      "unstructured": "Jack A., Ladner J. E., Rhodes D., Brown R. S., Klug A., J. Mol. Biol. 111, 315 (1977);",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "e_1_3_1_52_3",
      "doi-asserted-by": "crossref",
      "first-page": "2811",
      "DOI": "10.1093/nar/4.8.2811",
      "volume": "4",
      "author": "Holbrook S. R.",
      "year": "1977",
      "unstructured": "Holbrook S. R., Sussman J. L., Warrant R. W., Church G. M., Kim S. H., Nucleic Acids Res. 4, 2811 (1977).",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "e_1_3_1_53_2",
      "unstructured": "Cate J. H. Doudna J. A. in preparation."
    },
    {
      "key": "e_1_3_1_54_2",
      "unstructured": "The two molecules (A and B) in the asymmetric unit of the crystal show different degrees of order at the 5\u2032 end. In molecule B clear density is seen in the solvent-flattened experimental map for all but the first G of the sequence; in molecule A the density is weak for the first 4 nt of the sequence."
    },
    {
      "key": "e_1_3_1_55_2",
      "doi-asserted-by": "crossref",
      "first-page": "578",
      "DOI": "10.1038/347578a0",
      "volume": "347",
      "author": "Michel F.",
      "year": "1990",
      "unstructured": "Michel F., Ellington A. D., Couture S., Szostak J. W., Nature 347, 578 (1990).",
      "journal-title": "Nature"
    },
    {
      "key": "e_1_3_1_56_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.7682726"
    },
    {
      "key": "e_1_3_1_57_2",
      "doi-asserted-by": "crossref",
      "first-page": "391",
      "DOI": "10.1038/342391a0",
      "volume": "342",
      "author": "Michel F.",
      "year": "1989",
      "unstructured": "Michel F., Hanna M., Green R., Bartel D. P., Szostak J. W., Nature 342, 391 (1989).",
      "journal-title": "Nature"
    },
    {
      "key": "e_1_3_1_58_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.1315076"
    },
    {
      "key": "e_1_3_1_59_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/358123a0"
    },
    {
      "key": "e_1_3_1_60_2",
      "doi-asserted-by": "crossref",
      "first-page": "1201",
      "DOI": "10.1021/bi952244f",
      "volume": "35",
      "author": "Strobel S. A.",
      "year": "1996",
      "unstructured": "Strobel S. A., Cech T. R., Biochemistry 35, 1201 (1996).",
      "journal-title": "Biochemistry"
    },
    {
      "key": "e_1_3_1_61_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0022-2836(68)90392-6"
    },
    {
      "key": "e_1_3_1_62_2",
      "doi-asserted-by": "crossref",
      "first-page": "33",
      "DOI": "10.1016/0378-1119(93)90046-6",
      "volume": "135",
      "author": "Cech T. R.",
      "year": "1993",
      "unstructured": "Cech T. R., Gene 135, 33 (1993).",
      "journal-title": "Gene"
    },
    {
      "key": "e_1_3_1_63_2",
      "doi-asserted-by": "crossref",
      "first-page": "611",
      "DOI": "10.1038/375611a0",
      "volume": "375",
      "author": "Cuenoud B.",
      "year": "1995",
      "unstructured": "Cuenoud B., Szostak J. W., Nature 375, 611 (1995);",
      "journal-title": "Nature"
    },
    {
      "key": "e_1_3_1_63_3",
      "doi-asserted-by": "crossref",
      "first-page": "223",
      "DOI": "10.1016/1074-5521(94)90014-0",
      "volume": "1",
      "author": "Breaker R. R.",
      "year": "1994",
      "unstructured": "Breaker R. R. and , Joyce G. F., Chem. Biol. 1, 223 (1994);",
      "journal-title": "Chem. Biol."
    },
    {
      "key": "e_1_3_1_63_4",
      "first-page": "655",
      "volume": "2",
      "year": "1995",
      "unstructured": "ibid. 2, 655 (1995).",
      "journal-title": "ibid."
    },
    {
      "key": "e_1_3_1_64_2",
      "first-page": "80",
      "volume-title": "Isomorphous Replacement and Anomalous Scattering",
      "author": "Otwinowski Z.",
      "year": "1991",
      "unstructured": "Otwinowski Z., in Isomorphous Replacement and Anomalous Scattering, , Wolf W., Evans P. R., Leslie A. G. W., Eds. (SERC Daresbury Laboratory, Warington, UK, 1991), pp. 80-86."
    },
    {
      "key": "e_1_3_1_65_2",
      "doi-asserted-by": "crossref",
      "unstructured": "Acta Crystallogr. D vol. 50 (1994) p. 760Collaborative Computing Project Number 4.",
      "DOI": "10.1107/S0907444994003112"
    },
    {
      "key": "e_1_3_1_66_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1107/S0108767390010224"
    },
    {
      "key": "e_1_3_1_67_2",
      "volume-title": "X-PLOR Manual, Version 3.1: A System for X-ray Crystallography and NMR",
      "author": "Br\u00fcnger A.",
      "year": "1993",
      "unstructured": "Br\u00fcnger A., X-PLOR Manual, Version 3.1: A System for X-ray Crystallography and NMR (Yale Univ. Press, New Haven, CT, 1993)."
    },
    {
      "key": "e_1_3_1_68_2",
      "doi-asserted-by": "crossref",
      "first-page": "958",
      "DOI": "10.1107/S0021889891007240",
      "volume": "24",
      "author": "Carson M.",
      "year": "1991",
      "unstructured": "Carson M., J. Appl. Cryst. 24, 958 (1991).",
      "journal-title": "J. Appl. Cryst."
    },
    {
      "key": "e_1_3_1_69_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.8085157"
    },
    {
      "key": "e_1_3_1_70_2",
      "unstructured": "The MidasPlus program was developed at the Computer Graphics Laboratory University of California San Francisco (supported by NIH RR-01081)."
    },
    {
      "key": "e_1_3_1_71_2",
      "unstructured": "We thank H. Taube of Stanford University for the osmium hexammine triflate; T. Steitz S. Schultz A. Br\u00fcnger A. Ferr\u00e9-d'Amar\u00e9 C. Correll D. Engelman A. Friedman T. Griffin J. Jaeger A. M. Pyle V. Rath L. Rice L. Silvian S. Strobel J. Wang and members of the Center for Structural Biology at Yale for many helpful discussions; V. Carperos L. Doherty A. Ferr\u00e9-d'Amar\u00e9 C. Correll and J. Jaeger for help with data collection; V. Rath and Pfizer Inc. of Groton CT for use of data collection equipment; C. Ogata and W. Hendrickson for useful discussions and data collection time at beamline X-4A at the National Synchrotron Light Source Brookhaven National Laboratory Upton NY; the staff at Cornell High Energy Synchrotron Source (CHESS) beamline A-1; A. Thompson and the staff at beamline BL-19 at the European Synchrotron Radiation Facility (ESRF) Grenoble France; and A. Ferr\u00e9-d'Amar\u00e9 V. Rath and S. Strobel for review of the manuscript. Supported by the Lucille P. Markey Charitable Trust Scholars Program the Donaghue Medical Research Foundation NIH grant GM22778-21 the Searle Scholars Program and the Beckman Young Investigators Program (J.A.D.) NIH training grant 5T32GM08283-07 (J.H.C.) American Cancer Society postdoctoral fellowship (B.L.G.) NSF grant MCB-9221307 (C.E.K.) Howard Hughes Medical Institute (T.R.C.) and the Keck Foundation (C.E.K. and T.R.C.)."
    }
  ],
  "container-title": "Science",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://www.science.org/doi/pdf/10.1126/science.273.5282.1678",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2024,
        8,
        7
      ]
    ],
    "date-time": "2024-08-07T11:42:10Z",
    "timestamp": 1723030930000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://www.science.org/doi/10.1126/science.273.5282.1678"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        1996,
        9,
        20
      ]
    ]
  },
  "references-count": 76,
  "journal-issue": {
    "issue": "5282",
    "published-print": {
      "date-parts": [
        [
          1996,
          9,
          20
        ]
      ]
    }
  },
  "alternative-id": [
    "10.1126/science.273.5282.1678"
  ],
  "URL": "http://dx.doi.org/10.1126/science.273.5282.1678",
  "relation": {},
  "ISSN": [
    "0036-8075",
    "1095-9203"
  ],
  "subject": [],
  "container-title-short": "Science",
  "published": {
    "date-parts": [
      [
        1996,
        9,
        20
      ]
    ]
  }
}