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- PDB-5w0s: GroEL using cryoEM -

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Basic information

Entry
Database: PDB / ID: 5w0s
TitleGroEL using cryoEM
Components60 kDa chaperonin
KeywordsCHAPERONE / GroEL / cryoEM / conformational heterogeneity.
Function / homologyChaperonin Cpn60/TCP-1 family / GroEL-like apical domain superfamily / Chaperonins cpn60 signature. / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60 / GroEL-like equatorial domain superfamily / Chaperonin Cpn60, conserved site / TCP-1-like chaperonin intermediate domain superfamily / GroEL-GroES complex / 'de novo' protein folding ...Chaperonin Cpn60/TCP-1 family / GroEL-like apical domain superfamily / Chaperonins cpn60 signature. / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60 / GroEL-like equatorial domain superfamily / Chaperonin Cpn60, conserved site / TCP-1-like chaperonin intermediate domain superfamily / GroEL-GroES complex / 'de novo' protein folding / chaperone cofactor-dependent protein refolding / virion assembly / protein folding / response to radiation / unfolded protein binding / response to heat / protein refolding / ATPase activity / cell cycle / cell division / magnesium ion binding / membrane / ATP binding / identical protein binding / cytosol / cytoplasm / 60 kDa chaperonin / 60 kDa chaperonin
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.5 Å resolution
AuthorsRoh, S.H. / Chiu, W.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM.
Authors: Soung-Hun Roh / Corey F Hryc / Hyun-Hwan Jeong / Xue Fei / Joanita Jakana / George H Lorimer / Wah Chiu
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 31, 2017 / Release: Aug 9, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 9, 2017Structure modelrepositoryInitial release
1.1Aug 16, 2017Structure modelDatabase references / Refinement descriptioncitation / em_3d_fitting_citation.journal_volume / _citation.page_first / _citation.page_last
1.2Sep 20, 2017Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization

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Structure visualization

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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


Theoretical massNumber of molelcules
Total (without water)772,07214
Polyers772,07214
Non-polymers00
Water1,928107
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)51650
ΔGint (kcal/M)-195
Surface area (Å2)289180
MethodPISA

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Components

#1: Protein/peptide
60 kDa chaperonin / GroEL protein / Protein Cpn60


Mass: 55148.020 Da / Num. of mol.: 14 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mopA, groEL, groL / Production host: Escherichia coli (E. coli) / References: UniProt: Q6Q099, UniProt: P0A6F5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Formula: H2O / Water

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Wild type GroEL / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 800 kDa/nm / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.2
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyMicroscope model: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: RELION / Version: 1.4 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D7
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 37367 / Symmetry type: POINT
Atomic model buildingDetails: Regarding negative occupancies: To assess fit-to-density, we derived cross-correlations at the amino acid level and by means of a map/model FSC. To perform this assessment, we generated a weighted map, derived solely from an atomic model that accounted for both ADP of all atoms and weak/negative density of all charged oxygen atoms, and compared it with the experimental map. The weighted map provides a better approximation of the experimental map by simulating map variability as opposed to treating all atoms equally. The correlations for both the FSC and the per-residue assessment showed improvements when properly weighted, further demonstrating that our model provides a good approximation of the experimental data

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