+Open data
-Basic information
Entry | Database: PDB / ID: 5w0s | ||||||
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Title | GroEL using cryoEM | ||||||
Components | 60 kDa chaperonin | ||||||
Keywords | CHAPERONE / GroEL / cryoEM / conformational heterogeneity. | ||||||
Function / homology | Function and homology information GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / protein refolding ...GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / protein refolding / response to heat / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Roh, S.H. / Chiu, W. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 / Abstract: Single-particle electron cryo-microscopy (cryo-EM) is an emerging tool for resolving structures of conformationally heterogeneous particles; however, each structure is derived from an average of many ...Single-particle electron cryo-microscopy (cryo-EM) is an emerging tool for resolving structures of conformationally heterogeneous particles; however, each structure is derived from an average of many particles with presumed identical conformations. We used a 3.5-Å cryo-EM reconstruction with imposed D7 symmetry to further analyze structural heterogeneity among chemically identical subunits in each GroEL oligomer. Focused classification of the 14 subunits in each oligomer revealed three dominant classes of subunit conformations. Each class resembled a distinct GroEL crystal structure in the Protein Data Bank. The conformational differences stem from the orientations of the apical domain. We mapped each conformation class to its subunit locations within each GroEL oligomer in our dataset. The spatial distributions of each conformation class differed among oligomers, and most oligomers contained 10-12 subunits of the three dominant conformation classes. Adjacent subunits were found to more likely assume the same conformation class, suggesting correlation among subunits in the oligomer. This study demonstrates the utility of cryo-EM in revealing structure dynamics within a single protein oligomer. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5w0s.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5w0s.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 5w0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5w0s_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5w0s_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5w0s_validation.xml.gz | 187.8 KB | Display | |
Data in CIF | 5w0s_validation.cif.gz | 305.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/5w0s ftp://data.pdbj.org/pub/pdb/validation_reports/w0/5w0s | HTTPS FTP |
-Related structure data
Related structure data | 8750MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Number of models | 4 |
-Components
#1: Protein | Mass: 55148.020 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source 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 / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Wild type GroEL / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 800 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.2 |
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: JEOL 3200FSC |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software | Name: RELION / Version: 1.4 / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: D7 (2x7 fold dihedral) |
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37367 / Symmetry type: POINT |
Atomic model building | Details: 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 ...Details: 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 |