8WUW | pdb_00008wuw

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

PDB DOI: https://doi.org/10.2210/pdb8WUW/pdb
EM Map EMD-37862: EMDB EMDataResource

Classification: CHAPERONE
Organism(s): Hydrogenobacter thermophilus TK-6
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-10-21 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: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental, in silico
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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

PubMed: 38492570 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2024.02.012
Primary Citation 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: 949.11 kDa
Atom Count: 64,841
Modeled Residue Count: 8,540
Deposited Residue Count: 8,750
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperonin GroEL	A B [auth H] E [auth B] F [auth I] I [auth C] A, B [auth H], E [auth B], F [auth I], I [auth C], J, M [auth D], N [auth K], Q [auth E], R [auth L], U [auth F], V [auth M], Y [auth G], Z [auth N]	529	Hydrogenobacter thermophilus TK-6	Mutation(s): 0 Gene Names: groL, groEL, HTH_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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D3DK86
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Co-chaperonin GroES	AA [auth g] BA [auth n] C [auth a] D [auth h] G [auth b] AA [auth g], BA [auth n], C [auth a], D [auth h], G [auth b], H [auth i], K [auth c], L [auth j], O [auth d], P [auth k], S [auth e], T [auth l], W [auth f], X [auth m]	96	Hydrogenobacter thermophilus TK-6	Mutation(s): 0 Gene Names: groS, groES, HTH_1793
UniProt
Find proteins for D3DK85 (Hydrogenobacter thermophilus (strain DSM 6534 / IAM 12695 / TK-6)) Explore D3DK85 Go to UniProtKB: D3DK85
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D3DK85
Sequence Annotations Expand
Reference Sequence

Small Molecules

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