8WUW

Cryo-EM structure of H. thermophilus GroEL-GroES2 asymmetric football complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural insights into thermophilic chaperonin complexes.

Liao, Z.Gopalasingam, C.C.Kameya, M.Gerle, C.Shigematsu, H.Ishii, M.Arakawa, T.Fushinobu, S.

(2024) Structure 

  • DOI: https://doi.org/10.1016/j.str.2024.02.012
  • Primary Citation of Related Structures:  
    8WU4, 8WUC, 8WUW, 8WUX

  • PubMed Abstract: 

    Group I chaperonins are dual heptamer protein complexes that play significant roles in protein homeostasis. The structure and function of the Escherichia coli chaperonin are well characterized. However, the dynamic properties of chaperonins, such as large ATPase-dependent conformational changes by binding of lid-like co-chaperonin GroES, have made structural analyses challenging, and our understanding of these changes during the turnover of chaperonin complex formation is limited. In this study, we used single-particle cryogenic electron microscopy to investigate the structures of GroES-bound chaperonin complexes from the thermophilic hydrogen-oxidizing bacteria Hydrogenophilus thermoluteolus and Hydrogenobacter thermophilus in the presence of ATP and AMP-PNP. We captured the structure of an intermediate state chaperonin complex, designated as an asymmetric football-shaped complex, and performed analyses to decipher the dynamic structural variations. Our structural analyses of inter- and intra-subunit communications revealed a unique mechanism of complex formation through the binding of a second GroES to a bullet-shaped complex.


  • Organizational Affiliation

    Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo City, Tokyo 113-8654, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chaperonin GroEL529Hydrogenobacter thermophilus TK-6Mutation(s): 0 
Gene Names: groLgroELHTH_1794
EC: 5.6.1.7
UniProt
Find proteins for D3DK86 (Hydrogenobacter thermophilus (strain DSM 6534 / IAM 12695 / TK-6))
Explore D3DK86 
Go to UniProtKB:  D3DK86
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3DK86
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Co-chaperonin GroES96Hydrogenobacter thermophilus TK-6Mutation(s): 0 
Gene Names: groSgroESHTH_1793
UniProt
Find proteins for D3DK85 (Hydrogenobacter thermophilus (strain DSM 6534 / IAM 12695 / TK-6))
Explore D3DK85 
Go to UniProtKB:  D3DK85
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3DK85
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP (Subject of Investigation/LOI)
Query on ANP

Download Ideal Coordinates CCD File 
AB [auth L]
CB [auth F]
DA [auth A]
FB [auth M]
GA [auth H]
AB [auth L],
CB [auth F],
DA [auth A],
FB [auth M],
GA [auth H],
HB [auth G],
IA [auth B],
KB [auth N],
LA [auth I],
NA [auth C],
QA [auth J],
SA [auth D],
VA [auth K],
XA [auth E]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
K (Subject of Investigation/LOI)
Query on K

Download Ideal Coordinates CCD File 
EB [auth M]
FA [auth H]
JB [auth N]
KA [auth I]
PA [auth J]
EB [auth M],
FA [auth H],
JB [auth N],
KA [auth I],
PA [auth J],
UA [auth K],
ZA [auth L]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BB [auth F]
CA [auth A]
DB [auth M]
EA [auth H]
GB [auth G]
BB [auth F],
CA [auth A],
DB [auth M],
EA [auth H],
GB [auth G],
HA [auth B],
IB [auth N],
JA [auth I],
MA [auth C],
OA [auth J],
RA [auth D],
TA [auth K],
WA [auth E],
YA [auth L]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTISOLDE1.6
MODEL REFINEMENTPHENIX1.2
RECONSTRUCTIONcryoSPARC4.3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan23H00322
Japan Science and TechnologyJapanJPMJSP2108

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-27
    Type: Initial release