8WUC

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

PDB DOI: https://doi.org/10.2210/pdb8WUC/pdb
EM Map EMD-37853: EMDB EMDataResource

Classification: CHAPERONE
Organism(s): Hydrogenophilus thermoluteolus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-10-20 Released: 2024-03-27
Deposition Author(s): Liao, Z., Gopalasingam, C.C., Kameya, M., Gerle, C., Shigematsu, H., Ishii, M., Arakawa, T., Fushinobu, S.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

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 1.0 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

PubMed: 38492570 Search on PubMed
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.

Macromolecule Content

Total Structure Weight: 934.61 kDa
Atom Count: 65,338
Modelled Residue Count: 8,708
Deposited Residue Count: 8,708
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperonin GroEL	A AA [auth N] C [auth B] E [auth C] G [auth D] A, AA [auth N], C [auth B], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H], Q [auth I], S [auth J], U [auth K], W [auth L], Y [auth M]	528	Hydrogenophilus thermoluteolus	Mutation(s): 0 EC: 5.6.1.7
UniProt
Find proteins for A0A2Z6DW38 (Hydrogenophilus thermoluteolus) Explore A0A2Z6DW38 Go to UniProtKB: A0A2Z6DW38
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2Z6DW38
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Co-chaperonin GroES	B [auth a] BA [auth n] D [auth b] F [auth c] H [auth d] B [auth a], BA [auth n], D [auth b], F [auth c], H [auth d], J [auth e], L [auth f], N [auth g], P [auth h], R [auth i], T [auth j], V [auth k], X [auth l], Z [auth m]	94	Hydrogenophilus thermoluteolus	Mutation(s): 0 Gene Names: groES, groS, HPTL_0309
UniProt
Find proteins for A0A2Z6DVV7 (Hydrogenophilus thermoluteolus) Explore A0A2Z6DVV7 Go to UniProtKB: A0A2Z6DVV7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2Z6DVV7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain AB [auth M] SDF format, chain CA [auth A] SDF format, chain CB [auth N] SDF format, chain EA [auth B] SDF format, chain GA [auth C] SDF format, chain IA [auth D] SDF format, chain KA [auth E] SDF format, chain MA [auth F] SDF format, chain OA [auth G] SDF format, chain QA [auth H] SDF format, chain SA [auth I] SDF format, chain UA [auth J] SDF format, chain WA [auth K] SDF format, chain YA [auth L] MOL2 format, chain AB [auth M] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth N] MOL2 format, chain EA [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain KA [auth E] MOL2 format, chain MA [auth F] MOL2 format, chain OA [auth G] MOL2 format, chain QA [auth H] MOL2 format, chain SA [auth I] MOL2 format, chain UA [auth J] MOL2 format, chain WA [auth K] MOL2 format, chain YA [auth L]	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		Interactions Focus chain AB [auth M] Focus chain CA [auth A] Focus chain CB [auth N] Focus chain EA [auth B] Focus chain GA [auth C] Focus chain IA [auth D] Focus chain KA [auth E] Focus chain MA [auth F] Focus chain OA [auth G] Focus chain QA [auth H] Focus chain SA [auth I] Focus chain UA [auth J] Focus chain WA [auth K] Focus chain YA [auth L] Interactions & Density Focus chain AB [auth M] Focus chain CA [auth A] Focus chain CB [auth N] Focus chain EA [auth B] Focus chain GA [auth C] Focus chain IA [auth D] Focus chain KA [auth E] Focus chain MA [auth F] Focus chain OA [auth G] Focus chain QA [auth H] Focus chain SA [auth I] Focus chain UA [auth J] Focus chain WA [auth K] Focus chain YA [auth L]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain BB [auth M] SDF format, chain DA [auth A] SDF format, chain DB [auth N] SDF format, chain FA [auth B] SDF format, chain HA [auth C] SDF format, chain JA [auth D] SDF format, chain LA [auth E] SDF format, chain NA [auth F] SDF format, chain PA [auth G] SDF format, chain RA [auth H] SDF format, chain TA [auth I] SDF format, chain VA [auth J] SDF format, chain XA [auth K] SDF format, chain ZA [auth L] MOL2 format, chain BB [auth M] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth N] MOL2 format, chain FA [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain LA [auth E] MOL2 format, chain NA [auth F] MOL2 format, chain PA [auth G] MOL2 format, chain RA [auth H] MOL2 format, chain TA [auth I] MOL2 format, chain VA [auth J] MOL2 format, chain XA [auth K] MOL2 format, chain ZA [auth L]	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		Interactions Focus chain BB [auth M] Focus chain DA [auth A] Focus chain DB [auth N] Focus chain FA [auth B] Focus chain HA [auth C] Focus chain JA [auth D] Focus chain LA [auth E] Focus chain NA [auth F] Focus chain PA [auth G] Focus chain RA [auth H] Focus chain TA [auth I] Focus chain VA [auth J] Focus chain XA [auth K] Focus chain ZA [auth L] Interactions & Density Focus chain BB [auth M] Focus chain DA [auth A] Focus chain DB [auth N] Focus chain FA [auth B] Focus chain HA [auth C] Focus chain JA [auth D] Focus chain LA [auth E] Focus chain NA [auth F] Focus chain PA [auth G] Focus chain RA [auth H] Focus chain TA [auth I] Focus chain VA [auth J] Focus chain XA [auth K] Focus chain ZA [auth L]