8WUC

Cryo-EM structure of H. thermoluteolus GroEL-GroES2 football complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 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 32: 679-689.e4

  • 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 GroEL528Hydrogenophilus thermoluteolusMutation(s): 0 
EC: 5.6.1.7
UniProt
Find proteins for A0A2Z6DW38 (Hydrogenophilus thermoluteolus)
Explore A0A2Z6DW38 
Go to UniProtKB:  A0A2Z6DW38
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2Z6DW38
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 GroES94Hydrogenophilus thermoluteolusMutation(s): 0 
Gene Names: groESgroSHPTL_0309
UniProt
Find proteins for A0A2Z6DVV7 (Hydrogenophilus thermoluteolus)
Explore A0A2Z6DVV7 
Go to UniProtKB:  A0A2Z6DVV7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2Z6DVV7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
AB [auth M]
CA [auth A]
CB [auth N]
EA [auth B]
GA [auth C]
AB [auth M],
CA [auth A],
CB [auth N],
EA [auth B],
GA [auth C],
IA [auth D],
KA [auth E],
MA [auth F],
OA [auth G],
QA [auth H],
SA [auth I],
UA [auth J],
WA [auth K],
YA [auth L]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BB [auth M]
DA [auth A]
DB [auth N]
FA [auth B]
HA [auth C]
BB [auth M],
DA [auth A],
DB [auth N],
FA [auth B],
HA [auth C],
JA [auth D],
LA [auth E],
NA [auth F],
PA [auth G],
RA [auth H],
TA [auth I],
VA [auth J],
XA [auth K],
ZA [auth L]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
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
  • Version 1.1: 2024-06-19
    Changes: Database references