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- PDB-2c7d: Fitted coordinates for GroEL-ADP7-GroES Cryo-EM complex (EMD-1181) -

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Basic information

Entry
Database: PDB / ID: 2c7d
TitleFitted coordinates for GroEL-ADP7-GroES Cryo-EM complex (EMD-1181)
Components
  • 10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN
  • 60 KDA CHAPERONIN
KeywordsCHAPERONE / ATP-BINDING / ATOMIC STRUCTURE FITTING / CELL CYCLE / CELL DIVISION / CHAPERONIN / NUCLEOTIDE-BINDING / PHOSPHORYLATION
Function / homology
Function and homology information


GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding ...GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / protein-folding chaperone binding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / metal ion binding / cytosol
Similarity search - Function
Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily ...Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family / GroES-like superfamily
Similarity search - Domain/homology
Chaperonin GroEL / Co-chaperonin GroES
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsRanson, N.A. / Clare, D.K. / Farr, G.W. / Houldershaw, D. / Horwich, A.L. / Saibil, H.R.
CitationJournal: Nat Struct Mol Biol / Year: 2006
Title: Allosteric signaling of ATP hydrolysis in GroEL-GroES complexes.
Authors: Neil A Ranson / Daniel K Clare / George W Farr / David Houldershaw / Arthur L Horwich / Helen R Saibil /
Abstract: The double-ring chaperonin GroEL and its lid-like cochaperonin GroES form asymmetric complexes that, in the ATP-bound state, mediate productive folding in a hydrophilic, GroES-encapsulated chamber, ...The double-ring chaperonin GroEL and its lid-like cochaperonin GroES form asymmetric complexes that, in the ATP-bound state, mediate productive folding in a hydrophilic, GroES-encapsulated chamber, the so-called cis cavity. Upon ATP hydrolysis within the cis ring, the asymmetric complex becomes able to accept non-native polypeptides and ATP in the open, trans ring. Here we have examined the structural basis for this allosteric switch in activity by cryo-EM and single-particle image processing. ATP hydrolysis does not change the conformation of the cis ring, but its effects are transmitted through an inter-ring contact and cause domain rotations in the mobile trans ring. These rigid-body movements in the trans ring lead to disruption of its intra-ring contacts, expansion of the entire ring and opening of both the nucleotide pocket and the substrate-binding domains, admitting ATP and new substrate protein.
History
DepositionNov 22, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2006Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Version format compliance
Revision 1.2Aug 23, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.3Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.4May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-1181
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 60 KDA CHAPERONIN
B: 60 KDA CHAPERONIN
C: 60 KDA CHAPERONIN
D: 60 KDA CHAPERONIN
E: 60 KDA CHAPERONIN
F: 60 KDA CHAPERONIN
G: 60 KDA CHAPERONIN
H: 60 KDA CHAPERONIN
I: 60 KDA CHAPERONIN
J: 60 KDA CHAPERONIN
K: 60 KDA CHAPERONIN
L: 60 KDA CHAPERONIN
M: 60 KDA CHAPERONIN
N: 60 KDA CHAPERONIN
O: 10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN
P: 10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN
Q: 10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN
R: 10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN
S: 10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN
T: 10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN
U: 10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN


Theoretical massNumber of molelcules
Total (without water)874,45421
Polymers874,45421
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26510 Å2
ΔGint-484.6 kcal/mol
Surface area403090 Å2
MethodPISA

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Components

#1: Protein
60 KDA CHAPERONIN / GROEL / PROTEIN CPN60 / GROEL PROTEIN


Mass: 57260.504 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A6F5
#2: Protein
10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN


Mass: 10400.938 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A6F9

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: GROEL-ADP7-GROES / Type: COMPLEX
Buffer solutionName: 12.5MM HEPES, 5MM KCL, 5MM MGCL2 / pH: 7.5 / Details: 12.5MM HEPES, 5MM KCL, 5MM MGCL2
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 3300 nm / Nominal defocus min: 1400 nm / Cs: 2 mm
Specimen holderTemperature: 100 K
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 66
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1UROmodel fitting
2IMAGIC3D reconstruction
3SPIDER3D reconstruction
CTF correctionDetails: FULL CORRECTION ON 2D CLASS AVERAGES
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionMethod: PROJECTION MATCHING-BASED ANGULAR REFINEMENT OF MSA GENERATED CLASSES. ITERATIVE ALGEBRAIC RECONSTRUCTION IN SPIDER.
Resolution: 8.7 Å / Num. of particles: 7591 / Nominal pixel size: 1.4 Å
Details: RECIPROCAL SPACE FITTING OF SEVEN SEVEN INDEPENDENT RIGID BODIES WITH URO. FITTED ENTITIES WERE GROEL EQUATORIAL (RESIDUES 3-136 AND 410-524), INTERMEDIATE (RESIDUES 137-192 AND 374-409) AND ...Details: RECIPROCAL SPACE FITTING OF SEVEN SEVEN INDEPENDENT RIGID BODIES WITH URO. FITTED ENTITIES WERE GROEL EQUATORIAL (RESIDUES 3-136 AND 410-524), INTERMEDIATE (RESIDUES 137-192 AND 374-409) AND APICAL (RESIDUES 192-373) DOMAINS, PLUS A GROES SUBUNIT. THE MAP INTO WHICH THESE COORDINATES WERE FITTED IS AVAILABLE AT THE EMD (EMD-1181)
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Details: METHOD--RECIPROCAL SPACE FITTING IN URO
Atomic model buildingPDB-ID: 1AON

1aon


Accession code: 1AON / Source name: PDB / Type: experimental model
RefinementHighest resolution: 8.7 Å
Refinement stepCycle: LAST / Highest resolution: 8.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms57946 0 0 0 57946

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