DOI: 10.1016/j.str.2011.03.005. Cryo-EM Structure of a Group II Chaperonin in the Prehydrolysis ATP-Bound State Leading to Lid Closure

Cryo-EM Structure of a Group II Chaperonin in the Prehydrolysis ATP-Bound State Leading to Lid Closure

10.1016/j.str.2011.03.005

Crossref journal-article

Elsevier BV

Structure (78)

Bibliography

Zhang, J., Ma, B., DiMaio, F., Douglas, N. R., Joachimiak, L. A., Baker, D., Frydman, J., Levitt, M., & Chiu, W. (2011). Cryo-EM Structure of a Group II Chaperonin in the Prehydrolysis ATP-Bound State Leading to Lid Closure. Structure, 19(5), 633â639.

Authors 9

Junjie Zhang (first)
Boxue Ma (additional)
Frank DiMaio (additional)
Nicholai R. Douglas (additional)
Lukasz A. Joachimiak (additional)
David Baker (additional)
Judith Frydman (additional)
Michael Levitt (additional)
Wah Chiu (additional)

References 30 Referenced 51

10.1093/bioinformatics/bti770 / Bioinformatics / The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling by Arnold (2006)
10.1038/nprot.2010.126 / Nat. Protoc. / Cryo-EM of macromolecular assemblies at near-atomic resolution by Baker (2010)
10.1126/science.1141448 / Science / Adapting proteostasis for disease intervention by Balch (2008)
10.1038/nsmb.1436 / Nat. Struct. Mol. Biol. / Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT by Booth (2008)
10.1038/nsb1295-1083 / Nat. Struct. Biol. / Conformational variability in the refined structure of the chaperonin GroEL at 2.8 A resolution by Braig (1995)
10.1093/emboj/cdg477 / EMBO J. / Role of the gamma-phosphate of ATP in triggering protein folding by GroEL-GroES: function, structure and energetics by Chaudhry (2003)
10.1016/j.jmb.2004.07.015 / J. Mol. Biol. / Exploring the structural dynamics of the E.coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states by Chaudhry (2004)
10.1073/pnas.91.19.9111 / Proc. Natl. Acad. Sci. USA / Two yeast genes with similarity to TCP-1 are required for microtubule and actin function in vivo by Chen (1994)
10.1073/pnas.0913774107 / Proc. Natl. Acad. Sci. USA / 4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement by Cong (2010)
10.1016/j.jmb.2009.07.008 / J. Mol. Biol. / Refinement of protein structures into low-resolution density maps using rosetta by DiMaio (2009)
10.1016/S0092-8674(00)81152-6 / Cell / Crystal structure of the thermosome, the archaeal chaperonin and homolog of CCT by Ditzel (1998)
10.1016/j.semcdb.2003.12.008 / Semin. Cell Dev. Biol. / Principles of protein folding, misfolding and aggregation by Dobson (2004)
10.1016/j.cell.2010.12.017 / Cell / Dual action of ATP hydrolysis couples lid closure to substrate release into the group II chaperonin chamber by Douglas (2011)
10.1126/science.1068408 / Science / Molecular chaperones in the cytosol: from nascent chain to folded protein by Hartl (2002)
10.1016/j.jmb.2003.12.035 / J. Mol. Biol. / NMR studies on the substrate-binding domains of the thermosome: structural plasticity in the protrusion region by Heller (2004)
10.1002/pro.531 / Protein Sci. / The group II chaperonin Mm-Cpn binds and refolds human γD crystallin by Knee (2011)
10.1042/bj20030230 / Biochem. J. / Nucleotide-dependent protein folding in the type II chaperonin from the mesophilic archaeon Methanococcus maripaludis by Kusmierczyk (2003)
10.1006/jmbi.2000.4014 / J. Mol. Biol. / A dynamic model for the allosteric mechanism of GroEL by Ma (2000)
10.1074/jbc.M110.125344 / J. Biol. Chem. / Crystal structures of a group II chaperonin reveal the open and closed states associated with the protein folding cycle by Pereira (2010)
10.1002/jcc.20084 / J. Comput. Chem. / UCSF Chimera–a visualization system for exploratory research and analysis by Pettersen (2004)
10.1016/S0092-8674(01)00617-1 / Cell / ATP-bound states of GroEL captured by cryo-electron microscopy by Ranson (2001)
10.1038/nsmb1046 / Nat. Struct. Mol. Biol. / Allosteric signaling of ATP hydrolysis in GroEL-GroES complexes by Ranson (2006)
10.1038/nsmb1236 / Nat. Struct. Mol. Biol. / Essential function of the built-in lid in the allosteric regulation of eukaryotic and archaeal chaperonins by Reissmann (2007)
10.1111/j.1365-2818.1982.tb00405.x / J. Microsc. / The correlation averaging of a regularly arranged bacterial cell envelope protein by Saxton (1982)
10.1016/j.str.2007.09.021 / Structure / Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution by Schröder (2007)
10.1016/j.jmb.2003.11.028 / J. Mol. Biol. / Crystal structures of the group II chaperonin from Thermococcus strain KS-1: steric hindrance by the substituted amino acid, and inter-subunit rearrangement between two crystal forms by Shomura (2004)
10.1016/j.tcb.2004.09.015 / Trends Cell Biol. / Mechanism of the eukaryotic chaperonin: protein folding in the chamber of secrets by Spiess (2004)
10.1038/41944 / Nature / The crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex by Xu (1997)
10.1038/nsmb.1515 / Nat. Struct. Mol. Biol. / Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies by Yam (2008)
10.1038/nature08701 / Nature / Mechanism of folding chamber closure in a group II chaperonin by Zhang (2010)

Dates

Type	When
Created	14 years, 3 months ago (May 12, 2011, 10:30 a.m.)
Deposited	6 years, 8 months ago (Dec. 2, 2018, 4:22 p.m.)
Indexed	5 months ago (March 22, 2025, 5:26 a.m.)
Issued	14 years, 3 months ago (May 1, 2011)
Published	14 years, 3 months ago (May 1, 2011)
Published Print	14 years, 3 months ago (May 1, 2011)

Funders 0

None

BibTeX

@article{Zhang_2011, title={Cryo-EM Structure of a Group II Chaperonin in the Prehydrolysis ATP-Bound State Leading to Lid Closure}, volume={19}, ISSN={0969-2126}, url={http://dx.doi.org/10.1016/j.str.2011.03.005}, DOI={10.1016/j.str.2011.03.005}, number={5}, journal={Structure}, publisher={Elsevier BV}, author={Zhang, Junjie and Ma, Boxue and DiMaio, Frank and Douglas, Nicholai R. and Joachimiak, Lukasz A. and Baker, David and Frydman, Judith and Levitt, Michael and Chiu, Wah}, year={2011}, month=may, pages={633–639} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        3,
        22
      ]
    ],
    "date-time": "2025-03-22T09:26:47Z",
    "timestamp": 1742635607682
  },
  "reference-count": 30,
  "publisher": "Elsevier BV",
  "issue": "5",
  "license": [
    {
      "start": {
        "date-parts": [
          [
            2011,
            5,
            1
          ]
        ],
        "date-time": "2011-05-01T00:00:00Z",
        "timestamp": 1304208000000
      },
      "content-version": "tdm",
      "delay-in-days": 0,
      "URL": "https://www.elsevier.com/tdm/userlicense/1.0/"
    },
    {
      "start": {
        "date-parts": [
          [
            2013,
            8,
            22
          ]
        ],
        "date-time": "2013-08-22T00:00:00Z",
        "timestamp": 1377129600000
      },
      "content-version": "vor",
      "delay-in-days": 844,
      "URL": "https://www.elsevier.com/open-access/userlicense/1.0/"
    }
  ],
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        2011,
        5
      ]
    ]
  },
  "DOI": "10.1016/j.str.2011.03.005",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2011,
        5,
        12
      ]
    ],
    "date-time": "2011-05-12T14:30:53Z",
    "timestamp": 1305210653000
  },
  "page": "633-639",
  "source": "Crossref",
  "is-referenced-by-count": 51,
  "title": "Cryo-EM Structure of a Group II Chaperonin in the Prehydrolysis ATP-Bound State Leading to Lid Closure",
  "prefix": "10.1016",
  "volume": "19",
  "author": [
    {
      "given": "Junjie",
      "family": "Zhang",
      "sequence": "first",
      "affiliation": []
    },
    {
      "given": "Boxue",
      "family": "Ma",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Frank",
      "family": "DiMaio",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Nicholai\u00a0R.",
      "family": "Douglas",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Lukasz\u00a0A.",
      "family": "Joachimiak",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "David",
      "family": "Baker",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Judith",
      "family": "Frydman",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Michael",
      "family": "Levitt",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Wah",
      "family": "Chiu",
      "sequence": "additional",
      "affiliation": []
    }
  ],
  "member": "78",
  "reference": [
    {
      "key": "10.1016/j.str.2011.03.005_bib1",
      "doi-asserted-by": "crossref",
      "first-page": "195",
      "DOI": "10.1093/bioinformatics/bti770",
      "article-title": "The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling",
      "volume": "22",
      "author": "Arnold",
      "year": "2006",
      "journal-title": "Bioinformatics"
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib2",
      "doi-asserted-by": "crossref",
      "first-page": "1697",
      "DOI": "10.1038/nprot.2010.126",
      "article-title": "Cryo-EM of macromolecular assemblies at near-atomic resolution",
      "volume": "5",
      "author": "Baker",
      "year": "2010",
      "journal-title": "Nat. Protoc."
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib3",
      "doi-asserted-by": "crossref",
      "first-page": "916",
      "DOI": "10.1126/science.1141448",
      "article-title": "Adapting proteostasis for disease intervention",
      "volume": "319",
      "author": "Balch",
      "year": "2008",
      "journal-title": "Science"
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib4",
      "doi-asserted-by": "crossref",
      "first-page": "746",
      "DOI": "10.1038/nsmb.1436",
      "article-title": "Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT",
      "volume": "15",
      "author": "Booth",
      "year": "2008",
      "journal-title": "Nat. Struct. Mol. Biol."
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib5",
      "doi-asserted-by": "crossref",
      "first-page": "1083",
      "DOI": "10.1038/nsb1295-1083",
      "article-title": "Conformational variability in the refined structure of the chaperonin GroEL at 2.8 A resolution",
      "volume": "2",
      "author": "Braig",
      "year": "1995",
      "journal-title": "Nat. Struct. Biol."
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib6",
      "doi-asserted-by": "crossref",
      "first-page": "4877",
      "DOI": "10.1093/emboj/cdg477",
      "article-title": "Role of the gamma-phosphate of ATP in triggering protein folding by GroEL-GroES: function, structure and energetics",
      "volume": "22",
      "author": "Chaudhry",
      "year": "2003",
      "journal-title": "EMBO J."
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib7",
      "doi-asserted-by": "crossref",
      "first-page": "229",
      "DOI": "10.1016/j.jmb.2004.07.015",
      "article-title": "Exploring the structural dynamics of the E.coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states",
      "volume": "342",
      "author": "Chaudhry",
      "year": "2004",
      "journal-title": "J.\u00a0Mol. Biol."
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib8",
      "doi-asserted-by": "crossref",
      "first-page": "9111",
      "DOI": "10.1073/pnas.91.19.9111",
      "article-title": "Two yeast genes with similarity to TCP-1 are required for microtubule and actin function in\u00a0vivo",
      "volume": "91",
      "author": "Chen",
      "year": "1994",
      "journal-title": "Proc. Natl. Acad. Sci. USA"
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib9",
      "doi-asserted-by": "crossref",
      "first-page": "4967",
      "DOI": "10.1073/pnas.0913774107",
      "article-title": "4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement",
      "volume": "107",
      "author": "Cong",
      "year": "2010",
      "journal-title": "Proc. Natl. Acad. Sci. USA"
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib10",
      "doi-asserted-by": "crossref",
      "first-page": "181",
      "DOI": "10.1016/j.jmb.2009.07.008",
      "article-title": "Refinement of protein structures into low-resolution density maps using rosetta",
      "volume": "392",
      "author": "DiMaio",
      "year": "2009",
      "journal-title": "J.\u00a0Mol. Biol."
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib11",
      "doi-asserted-by": "crossref",
      "first-page": "125",
      "DOI": "10.1016/S0092-8674(00)81152-6",
      "article-title": "Crystal structure of the thermosome, the archaeal chaperonin and homolog of CCT",
      "volume": "93",
      "author": "Ditzel",
      "year": "1998",
      "journal-title": "Cell"
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib12",
      "doi-asserted-by": "crossref",
      "first-page": "3",
      "DOI": "10.1016/j.semcdb.2003.12.008",
      "article-title": "Principles of protein folding, misfolding and aggregation",
      "volume": "15",
      "author": "Dobson",
      "year": "2004",
      "journal-title": "Semin. Cell Dev. Biol."
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib13",
      "doi-asserted-by": "crossref",
      "first-page": "240",
      "DOI": "10.1016/j.cell.2010.12.017",
      "article-title": "Dual action of ATP hydrolysis couples lid closure to substrate release into the group II chaperonin chamber",
      "volume": "144",
      "author": "Douglas",
      "year": "2011",
      "journal-title": "Cell"
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib14",
      "doi-asserted-by": "crossref",
      "first-page": "1852",
      "DOI": "10.1126/science.1068408",
      "article-title": "Molecular chaperones in the cytosol: from nascent chain to folded protein",
      "volume": "295",
      "author": "Hartl",
      "year": "2002",
      "journal-title": "Science"
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib15",
      "doi-asserted-by": "crossref",
      "first-page": "717",
      "DOI": "10.1016/j.jmb.2003.12.035",
      "article-title": "NMR studies on the substrate-binding domains of the thermosome: structural plasticity in the protrusion region",
      "volume": "336",
      "author": "Heller",
      "year": "2004",
      "journal-title": "J.\u00a0Mol. Biol."
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib16",
      "doi-asserted-by": "crossref",
      "first-page": "30",
      "DOI": "10.1002/pro.531",
      "article-title": "The group II chaperonin Mm-Cpn binds and refolds human \u03b3D crystallin",
      "volume": "20",
      "author": "Knee",
      "year": "2011",
      "journal-title": "Protein Sci."
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib17",
      "doi-asserted-by": "crossref",
      "first-page": "669",
      "DOI": "10.1042/bj20030230",
      "article-title": "Nucleotide-dependent protein folding in the type II chaperonin from the mesophilic archaeon Methanococcus maripaludis",
      "volume": "371",
      "author": "Kusmierczyk",
      "year": "2003",
      "journal-title": "Biochem. J."
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib18",
      "doi-asserted-by": "crossref",
      "first-page": "303",
      "DOI": "10.1006/jmbi.2000.4014",
      "article-title": "A dynamic model for the allosteric mechanism of GroEL",
      "volume": "302",
      "author": "Ma",
      "year": "2000",
      "journal-title": "J.\u00a0Mol. Biol."
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib19",
      "doi-asserted-by": "crossref",
      "first-page": "27958",
      "DOI": "10.1074/jbc.M110.125344",
      "article-title": "Crystal structures of a group II chaperonin reveal the open and closed states associated with the protein folding cycle",
      "volume": "285",
      "author": "Pereira",
      "year": "2010",
      "journal-title": "J.\u00a0Biol. Chem."
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib20",
      "doi-asserted-by": "crossref",
      "first-page": "1605",
      "DOI": "10.1002/jcc.20084",
      "article-title": "UCSF Chimera\u2013a visualization system for exploratory research and analysis",
      "volume": "25",
      "author": "Pettersen",
      "year": "2004",
      "journal-title": "J.\u00a0Comput. Chem."
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib21",
      "doi-asserted-by": "crossref",
      "first-page": "869",
      "DOI": "10.1016/S0092-8674(01)00617-1",
      "article-title": "ATP-bound states of GroEL captured by cryo-electron microscopy",
      "volume": "107",
      "author": "Ranson",
      "year": "2001",
      "journal-title": "Cell"
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib22",
      "doi-asserted-by": "crossref",
      "first-page": "147",
      "DOI": "10.1038/nsmb1046",
      "article-title": "Allosteric signaling of ATP hydrolysis in GroEL-GroES complexes",
      "volume": "13",
      "author": "Ranson",
      "year": "2006",
      "journal-title": "Nat. Struct. Mol. Biol."
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib23",
      "doi-asserted-by": "crossref",
      "first-page": "432",
      "DOI": "10.1038/nsmb1236",
      "article-title": "Essential function of the built-in lid in the allosteric regulation of eukaryotic and archaeal chaperonins",
      "volume": "14",
      "author": "Reissmann",
      "year": "2007",
      "journal-title": "Nat. Struct. Mol. Biol."
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib24",
      "doi-asserted-by": "crossref",
      "first-page": "127",
      "DOI": "10.1111/j.1365-2818.1982.tb00405.x",
      "article-title": "The correlation averaging of a regularly arranged bacterial cell envelope protein",
      "volume": "127",
      "author": "Saxton",
      "year": "1982",
      "journal-title": "J.\u00a0Microsc."
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib25",
      "doi-asserted-by": "crossref",
      "first-page": "1630",
      "DOI": "10.1016/j.str.2007.09.021",
      "article-title": "Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution",
      "volume": "15",
      "author": "Schr\u00f6der",
      "year": "2007",
      "journal-title": "Structure"
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib26",
      "doi-asserted-by": "crossref",
      "first-page": "1265",
      "DOI": "10.1016/j.jmb.2003.11.028",
      "article-title": "Crystal structures of the group II chaperonin from Thermococcus strain KS-1: steric hindrance by the substituted amino acid, and inter-subunit rearrangement between two crystal forms",
      "volume": "335",
      "author": "Shomura",
      "year": "2004",
      "journal-title": "J.\u00a0Mol. Biol."
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib27",
      "doi-asserted-by": "crossref",
      "first-page": "598",
      "DOI": "10.1016/j.tcb.2004.09.015",
      "article-title": "Mechanism of the eukaryotic chaperonin: protein folding in the chamber of secrets",
      "volume": "14",
      "author": "Spiess",
      "year": "2004",
      "journal-title": "Trends Cell Biol."
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib28",
      "doi-asserted-by": "crossref",
      "first-page": "741",
      "DOI": "10.1038/41944",
      "article-title": "The crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex",
      "volume": "388",
      "author": "Xu",
      "year": "1997",
      "journal-title": "Nature"
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib29",
      "doi-asserted-by": "crossref",
      "first-page": "1255",
      "DOI": "10.1038/nsmb.1515",
      "article-title": "Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies",
      "volume": "15",
      "author": "Yam",
      "year": "2008",
      "journal-title": "Nat. Struct. Mol. Biol."
    },
    {
      "key": "10.1016/j.str.2011.03.005_bib30",
      "doi-asserted-by": "crossref",
      "first-page": "379",
      "DOI": "10.1038/nature08701",
      "article-title": "Mechanism of folding chamber closure in a group II chaperonin",
      "volume": "463",
      "author": "Zhang",
      "year": "2010",
      "journal-title": "Nature"
    }
  ],
  "container-title": "Structure",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://api.elsevier.com/content/article/PII:S096921261100102X?httpAccept=text/xml",
      "content-type": "text/xml",
      "content-version": "vor",
      "intended-application": "text-mining"
    },
    {
      "URL": "https://api.elsevier.com/content/article/PII:S096921261100102X?httpAccept=text/plain",
      "content-type": "text/plain",
      "content-version": "vor",
      "intended-application": "text-mining"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2018,
        12,
        2
      ]
    ],
    "date-time": "2018-12-02T21:22:48Z",
    "timestamp": 1543785768000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://linkinghub.elsevier.com/retrieve/pii/S096921261100102X"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2011,
        5
      ]
    ]
  },
  "references-count": 30,
  "journal-issue": {
    "issue": "5",
    "published-print": {
      "date-parts": [
        [
          2011,
          5
        ]
      ]
    }
  },
  "alternative-id": [
    "S096921261100102X"
  ],
  "URL": "http://dx.doi.org/10.1016/j.str.2011.03.005",
  "relation": {},
  "ISSN": [
    "0969-2126"
  ],
  "subject": [],
  "container-title-short": "Structure",
  "published": {
    "date-parts": [
      [
        2011,
        5
      ]
    ]
  }
}