[English] 日本語
Yorodumi
- PDB-7ywy: Structure of the GroEL chaperonin in complex with the CnoX chaper... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ywy
TitleStructure of the GroEL chaperonin in complex with the CnoX chaperedoxin
Components
  • Chaperedoxin
  • Chaperonin GroEL
KeywordsCHAPERONE / Protein Folding / Redox / Complex / Chaperonin
Function / homology: / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsVan der Verren, S.E. / Remaut, H. / Collet, J.F. / Dupuy, E.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0G0818N Belgium
Fonds de la Recherche Scientifique (FNRS)WELBIO-CR-2019C-03 Belgium
CitationJournal: 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
DepositionFeb 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
a: Chaperedoxin
b: Chaperonin GroEL
A: Chaperedoxin
G: Chaperonin GroEL
B: Chaperedoxin
H: Chaperonin GroEL
C: Chaperedoxin
I: Chaperonin GroEL
D: Chaperedoxin
J: Chaperonin GroEL
E: Chaperedoxin
K: Chaperonin GroEL
F: Chaperedoxin
L: Chaperonin GroEL
Y: Chaperedoxin
Z: Chaperonin GroEL
M: Chaperedoxin
S: Chaperonin GroEL
N: Chaperedoxin
T: Chaperonin GroEL
O: Chaperedoxin
U: Chaperonin GroEL
P: Chaperedoxin
V: Chaperonin GroEL
Q: Chaperedoxin
W: Chaperonin GroEL
R: Chaperedoxin
X: Chaperonin GroEL


Theoretical massNumber of molelcules
Total (without water)909,88828
Polymers909,88828
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The 14:1 stochiometric complex of GroEL:CnoX was proven by gel filtration, a CnoX-overdosed sample was prepared for single particle cryo-EM, mass spectrometry, in vivo pull ...Evidence: gel filtration, The 14:1 stochiometric complex of GroEL:CnoX was proven by gel filtration, a CnoX-overdosed sample was prepared for single particle cryo-EM, mass spectrometry, in vivo pull down of CnoX confirmed GroEL as the only partner, assay for oligomerization, Direct interaction parameters were measured using both AFM and fluorescence anisotropy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area51470 Å2
ΔGint-359 kcal/mol
Surface area420800 Å2

-
Components

#1: Protein
Chaperedoxin


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
Chaperonin GroEL


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

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 1:1 stoichiometric complex of GroEL-CnoX / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8 / Details: 50mM Tris pH=8, 150mM NaCl, 1mM EDTA
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Strep-affinity purified complex
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE

-
Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal magnification: 60000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 68.3 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1crYOLO1.5particle selection
2SerialEM3.8image acquisition
4CTFFIND4.1CTF correction
7Coot0.9.5model fitting
9RELION3initial Euler assignment
10RELION3final Euler assignment
11RELION3classification
12RELION33D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 670080
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 170458 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coeficient
Atomic model building
IDPDB-ID 3D fitting-ID
11GRL

1grl

1
23QOU

3qou

1

+
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://pdbjlvh1.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