[English] 日本語
Yorodumi
- PDB-2c7c: FITTED COORDINATES FOR GROEL-ATP7-GROES CRYO-EM COMPLEX (EMD-1180) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2c7c
TitleFITTED COORDINATES FOR GROEL-ATP7-GROES CRYO-EM COMPLEX (EMD-1180)
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 / response to heat / protein-folding chaperone binding / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / identical protein 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: 7.7 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 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.4Oct 2, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.5Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
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.

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-1180
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area62390 Å2
ΔGint-390.12 kcal/mol
Surface area321960 Å2
MethodPISA

-
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

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: GROEL-ATP7-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

-
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 FIELDBright-field microscopy / Nominal magnification: 50000 X / Nominal defocus max: 3200 nm / Nominal defocus min: 1100 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: 189
Radiation wavelengthRelative weight: 1

-
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: 7.7 Å / Num. of particles: 16281 / Nominal pixel size: 1.4 Å
Details: RECIPROCAL SPACE FITTING OF 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 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-1180)
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Details: METHOD--RECIPROCAL SPACE FITTING IN URO
RefinementHighest resolution: 7.7 Å
Refinement stepCycle: LAST / Highest resolution: 7.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms57946 0 0 0 57946

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more