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Yorodumi- PDB-7ywy: Structure of the GroEL chaperonin in complex with the CnoX chaper... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ywy | |||||||||
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Title | Structure of the GroEL chaperonin in complex with the CnoX chaperedoxin | |||||||||
Components |
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Keywords | CHAPERONE / Protein Folding / Redox / Complex / Chaperonin | |||||||||
Function / homology | : / : Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Van der Verren, S.E. / Remaut, H. / Collet, J.F. / Dupuy, E. | |||||||||
Funding support | Belgium, 2items
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Citation | Journal: Cell / Year: 2023 Title: A molecular device for the redox quality control of GroEL/ES substrates. Authors: Emile Dupuy / Sander Egbert Van der Verren / Jiusheng Lin / Mark Alan Wilson / Alix Vincent Dachsbeck / Felipe Viela / Emmanuelle Latour / Alexandra Gennaris / Didier Vertommen / Yves ...Authors: Emile Dupuy / Sander Egbert Van der Verren / Jiusheng Lin / Mark Alan Wilson / Alix Vincent Dachsbeck / Felipe Viela / Emmanuelle Latour / Alexandra Gennaris / Didier Vertommen / Yves Frédéric Dufrêne / Bogdan Iuliu Iorga / Camille Véronique Goemans / Han Remaut / Jean-François Collet / Abstract: Hsp60 chaperonins and their Hsp10 cofactors assist protein folding in all living cells, constituting the paradigmatic example of molecular chaperones. Despite extensive investigations of their ...Hsp60 chaperonins and their Hsp10 cofactors assist protein folding in all living cells, constituting the paradigmatic example of molecular chaperones. Despite extensive investigations of their structure and mechanism, crucial questions regarding how these chaperonins promote folding remain unsolved. Here, we report that the bacterial Hsp60 chaperonin GroEL forms a stable, functionally relevant complex with the chaperedoxin CnoX, a protein combining a chaperone and a redox function. Binding of GroES (Hsp10 cofactor) to GroEL induces CnoX release. Cryoelectron microscopy provided crucial structural information on the GroEL-CnoX complex, showing that CnoX binds GroEL outside the substrate-binding site via a highly conserved C-terminal α-helix. Furthermore, we identified complexes in which CnoX, bound to GroEL, forms mixed disulfides with GroEL substrates, indicating that CnoX likely functions as a redox quality-control plugin for GroEL. Proteins sharing structural features with CnoX exist in eukaryotes, suggesting that Hsp60 molecular plugins have been conserved through evolution. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ywy.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7ywy.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 7ywy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ywy_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7ywy_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7ywy_validation.xml.gz | 201.2 KB | Display | |
Data in CIF | 7ywy_validation.cif.gz | 312.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/7ywy ftp://data.pdbj.org/pub/pdb/validation_reports/yw/7ywy | HTTPS FTP |
-Related structure data
Related structure data | 14352MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 9771.923 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cnoX, GHT02_06645 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U2VUH6 #2: Protein | Mass: 55220.105 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: groL, AMK64_004370 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A828EVF1 |
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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: 1:1 stoichiometric complex of GroEL-CnoX / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 / Details: 50mM Tris pH=8, 150mM NaCl, 1mM EDTA |
Specimen | Conc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Strep-affinity purified complex |
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Nominal magnification: 60000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 68.3 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 670080 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C7 (7 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 170458 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coeficient | ||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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