9ES2 | pdb_00009es2

ATP-bound human mitochondrial Hsp60 double-ring complex

PDB DOI: https://doi.org/10.2210/pdb9ES2/pdb
EM Map EMD-19932: EMDB EMDataResource

Classification: CHAPERONE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-25 Released: 2025-04-09
Deposition Author(s): Lopez-Alonso, J.P., Tascon, I., Ubarretxena-Belandia, I.
Funding Organization(s): United States - Israel Binational Science Foundation (BSF), Spanish Ministry of Science, Innovation, and Universities, Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.44 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural basis for ATP-triggered assembly of human mitochondrial Hsp60-Hsp10 chaperonin

Tascon, I., Lopez-Alonso, J.P., Ubarretxena-Belandia, I., Vilchez, J., Shkolnisky, Y., Azem, A., Hirsch, J.

To be published.

Macromolecule Content

Total Structure Weight: 822.49 kDa
Atom Count: 58,254
Modeled Residue Count: 7,378
Deposited Residue Count: 7,686
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
60 kDa heat shock protein, mitochondrial	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	549	Homo sapiens	Mutation(s): 0 Gene Names: HSPD1, HSP60 EC: 3.6.4.9 (PDB Primary Data), 5.6.1.7 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P10809 (Homo sapiens) Explore P10809 Go to UniProtKB: P10809
PHAROS: P10809 GTEx: ENSG00000144381
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10809
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BB [auth N] SDF format, chain DA [auth F] SDF format, chain GA [auth G] SDF format, chain JA [auth H] SDF format, chain MA [auth I] SDF format, chain O [auth A] SDF format, chain PA [auth J] SDF format, chain R [auth B] SDF format, chain SA [auth K] SDF format, chain U [auth C] SDF format, chain VA [auth L] SDF format, chain X [auth D] SDF format, chain YA [auth M] MOL2 format, chain AA [auth E] MOL2 format, chain BB [auth N] MOL2 format, chain DA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain JA [auth H] MOL2 format, chain MA [auth I] MOL2 format, chain O [auth A] MOL2 format, chain PA [auth J] MOL2 format, chain R [auth B] MOL2 format, chain SA [auth K] MOL2 format, chain U [auth C] MOL2 format, chain VA [auth L] MOL2 format, chain X [auth D] MOL2 format, chain YA [auth M] mmCIF format, chain AA [auth E] mmCIF format, chain BB [auth N] mmCIF format, chain DA [auth F] mmCIF format, chain GA [auth G] mmCIF format, chain JA [auth H] mmCIF format, chain MA [auth I] mmCIF format, chain O [auth A] mmCIF format, chain PA [auth J] mmCIF format, chain R [auth B] mmCIF format, chain SA [auth K] mmCIF format, chain U [auth C] mmCIF format, chain VA [auth L] mmCIF format, chain X [auth D] mmCIF format, chain YA [auth M]	AA [auth E] BB [auth N] DA [auth F] GA [auth G] JA [auth H] AA [auth E], BB [auth N], DA [auth F], GA [auth G], JA [auth H], MA [auth I], O [auth A], PA [auth J], R [auth B], SA [auth K], U [auth C], VA [auth L], X [auth D], YA [auth M]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain AA [auth E] Focus chain BB [auth N] Focus chain DA [auth F] Focus chain GA [auth G] Focus chain JA [auth H] Focus chain MA [auth I] Focus chain O [auth A] Focus chain PA [auth J] Focus chain R [auth B] Focus chain SA [auth K] Focus chain U [auth C] Focus chain VA [auth L] Focus chain X [auth D] Focus chain YA [auth M] Interactions & Density Focus chain AA [auth E] Focus chain BB [auth N] Focus chain DA [auth F] Focus chain GA [auth G] Focus chain JA [auth H] Focus chain MA [auth I] Focus chain O [auth A] Focus chain PA [auth J] Focus chain R [auth B] Focus chain SA [auth K] Focus chain U [auth C] Focus chain VA [auth L] Focus chain X [auth D] Focus chain YA [auth M]
K Query on K Download Ideal Coordinates CCD File SDF format, chain AB [auth M] SDF format, chain CA [auth E] SDF format, chain DB [auth N] SDF format, chain FA [auth F] SDF format, chain IA [auth G] SDF format, chain LA [auth H] SDF format, chain OA [auth I] SDF format, chain Q [auth A] SDF format, chain RA [auth J] SDF format, chain T [auth B] SDF format, chain UA [auth K] SDF format, chain W [auth C] SDF format, chain XA [auth L] SDF format, chain Z [auth D] MOL2 format, chain AB [auth M] MOL2 format, chain CA [auth E] MOL2 format, chain DB [auth N] MOL2 format, chain FA [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain LA [auth H] MOL2 format, chain OA [auth I] MOL2 format, chain Q [auth A] MOL2 format, chain RA [auth J] MOL2 format, chain T [auth B] MOL2 format, chain UA [auth K] MOL2 format, chain W [auth C] MOL2 format, chain XA [auth L] MOL2 format, chain Z [auth D] mmCIF format, chain AB [auth M] mmCIF format, chain CA [auth E] mmCIF format, chain DB [auth N] mmCIF format, chain FA [auth F] mmCIF format, chain IA [auth G] mmCIF format, chain LA [auth H] mmCIF format, chain OA [auth I] mmCIF format, chain Q [auth A] mmCIF format, chain RA [auth J] mmCIF format, chain T [auth B] mmCIF format, chain UA [auth K] mmCIF format, chain W [auth C] mmCIF format, chain XA [auth L] mmCIF format, chain Z [auth D]	AB [auth M] CA [auth E] DB [auth N] FA [auth F] IA [auth G] AB [auth M], CA [auth E], DB [auth N], FA [auth F], IA [auth G], LA [auth H], OA [auth I], Q [auth A], RA [auth J], T [auth B], UA [auth K], W [auth C], XA [auth L], Z [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AB [auth M] Focus chain CA [auth E] Focus chain DB [auth N] Focus chain FA [auth F] Focus chain IA [auth G] Focus chain LA [auth H] Focus chain OA [auth I] Focus chain Q [auth A] Focus chain RA [auth J] Focus chain T [auth B] Focus chain UA [auth K] Focus chain W [auth C] Focus chain XA [auth L] Focus chain Z [auth D] Interactions & Density Focus chain AB [auth M] Focus chain CA [auth E] Focus chain DB [auth N] Focus chain FA [auth F] Focus chain IA [auth G] Focus chain LA [auth H] Focus chain OA [auth I] Focus chain Q [auth A] Focus chain RA [auth J] Focus chain T [auth B] Focus chain UA [auth K] Focus chain W [auth C] Focus chain XA [auth L] Focus chain Z [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain CB [auth N] SDF format, chain EA [auth F] SDF format, chain HA [auth G] SDF format, chain KA [auth H] SDF format, chain NA [auth I] SDF format, chain P [auth A] SDF format, chain QA [auth J] SDF format, chain S [auth B] SDF format, chain TA [auth K] SDF format, chain V [auth C] SDF format, chain WA [auth L] SDF format, chain Y [auth D] SDF format, chain ZA [auth M] MOL2 format, chain BA [auth E] MOL2 format, chain CB [auth N] MOL2 format, chain EA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain KA [auth H] MOL2 format, chain NA [auth I] MOL2 format, chain P [auth A] MOL2 format, chain QA [auth J] MOL2 format, chain S [auth B] MOL2 format, chain TA [auth K] MOL2 format, chain V [auth C] MOL2 format, chain WA [auth L] MOL2 format, chain Y [auth D] MOL2 format, chain ZA [auth M] mmCIF format, chain BA [auth E] mmCIF format, chain CB [auth N] mmCIF format, chain EA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain KA [auth H] mmCIF format, chain NA [auth I] mmCIF format, chain P [auth A] mmCIF format, chain QA [auth J] mmCIF format, chain S [auth B] mmCIF format, chain TA [auth K] mmCIF format, chain V [auth C] mmCIF format, chain WA [auth L] mmCIF format, chain Y [auth D] mmCIF format, chain ZA [auth M]	BA [auth E] CB [auth N] EA [auth F] HA [auth G] KA [auth H] BA [auth E], CB [auth N], EA [auth F], HA [auth G], KA [auth H], NA [auth I], P [auth A], QA [auth J], S [auth B], TA [auth K], V [auth C], WA [auth L], Y [auth D], ZA [auth M]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain CB [auth N] Focus chain EA [auth F] Focus chain HA [auth G] Focus chain KA [auth H] Focus chain NA [auth I] Focus chain P [auth A] Focus chain QA [auth J] Focus chain S [auth B] Focus chain TA [auth K] Focus chain V [auth C] Focus chain WA [auth L] Focus chain Y [auth D] Focus chain ZA [auth M] Interactions & Density Focus chain BA [auth E] Focus chain CB [auth N] Focus chain EA [auth F] Focus chain HA [auth G] Focus chain KA [auth H] Focus chain NA [auth I] Focus chain P [auth A] Focus chain QA [auth J] Focus chain S [auth B] Focus chain TA [auth K] Focus chain V [auth C] Focus chain WA [auth L] Focus chain Y [auth D] Focus chain ZA [auth M]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.44 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1
MODEL REFINEMENT	Coot	0.9.1
RECONSTRUCTION	cryoSPARC	3.3.1

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-09

Deposition Author(s):

Lopez-Alonso, J.P.

Tascon, I.

Ubarretxena-Belandia, I.

Funding Organization	Location	Grant Number
United States - Israel Binational Science Foundation (BSF)	United States	--
Spanish Ministry of Science, Innovation, and Universities	Spain	--
Other government		--