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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: To Be Published Title: A molecular plugin rescues GroEL/ES substrates from pre-folding oxidation Authors: Dupuy, E. / Van der Verren, S.E. / Lin, J. / Wilson, M. / Viela, F. / Latour, E. / Dachsbeck, A. / Gennaris, A. / Vertommen, D. / Dufresne, Y. / Iorga, B. / Goemans, C.V. / Remaut, H. / Collet, J.F. | |||||||||
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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