9ES1 | pdb_00009es1

ATP-bound human mitochondrial Hsp60-Hsp10 half football complex

PDB DOI: https://doi.org/10.2210/pdb9ES1/pdb
EM Map EMD-19931: 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: 2.95 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: 487.87 kDa
Atom Count: 35,636
Modelled Residue Count: 4,389
Deposited Residue Count: 4,557
Unique protein chains: 2

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 C [auth B] E [auth C] G [auth D] I [auth E] A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G]	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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
10 kDa heat shock protein, mitochondrial	B [auth a] D [auth b] F [auth c] H [auth d] J [auth e] B [auth a], D [auth b], F [auth c], H [auth d], J [auth e], L [auth f], N [auth g]	102	Homo sapiens	Mutation(s): 0 Gene Names: HSPE1
UniProt & NIH Common Fund Data Resources
Find proteins for P61604 (Homo sapiens) Explore P61604 Go to UniProtKB: P61604
PHAROS: P61604 GTEx: ENSG00000115541
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61604
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 DA [auth F] SDF format, chain GA [auth G] SDF format, chain O [auth A] SDF format, chain R [auth B] SDF format, chain U [auth C] SDF format, chain X [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] MOL2 format, chain X [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain GA [auth G] mmCIF format, chain O [auth A] mmCIF format, chain R [auth B] mmCIF format, chain U [auth C] mmCIF format, chain X [auth D]	AA [auth E] DA [auth F] GA [auth G] O [auth A] R [auth B] AA [auth E], DA [auth F], GA [auth G], O [auth A], R [auth B], U [auth C], X [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain AA [auth E] Focus chain DA [auth F] Focus chain GA [auth G] Focus chain O [auth A] Focus chain R [auth B] Focus chain U [auth C] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth F] Focus chain GA [auth G] Focus chain O [auth A] Focus chain R [auth B] Focus chain U [auth C] Focus chain X [auth D]
K Query on K Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain FA [auth F] SDF format, chain IA [auth G] SDF format, chain Q [auth A] SDF format, chain T [auth B] SDF format, chain W [auth C] SDF format, chain Z [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain T [auth B] MOL2 format, chain W [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain CA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain IA [auth G] mmCIF format, chain Q [auth A] mmCIF format, chain T [auth B] mmCIF format, chain W [auth C] mmCIF format, chain Z [auth D]	CA [auth E] FA [auth F] IA [auth G] Q [auth A] T [auth B] CA [auth E], FA [auth F], IA [auth G], Q [auth A], T [auth B], W [auth C], Z [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain FA [auth F] Focus chain IA [auth G] Focus chain Q [auth A] Focus chain T [auth B] Focus chain W [auth C] Focus chain Z [auth D] Interactions & Density Focus chain CA [auth E] Focus chain FA [auth F] Focus chain IA [auth G] Focus chain Q [auth A] Focus chain T [auth B] Focus chain W [auth C] Focus chain Z [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain EA [auth F] SDF format, chain HA [auth G] SDF format, chain P [auth A] SDF format, chain S [auth B] SDF format, chain V [auth C] SDF format, chain Y [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain P [auth A] MOL2 format, chain S [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain P [auth A] mmCIF format, chain S [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth D]	BA [auth E] EA [auth F] HA [auth G] P [auth A] S [auth B] BA [auth E], EA [auth F], HA [auth G], P [auth A], S [auth B], V [auth C], Y [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain EA [auth F] Focus chain HA [auth G] Focus chain P [auth A] Focus chain S [auth B] Focus chain V [auth C] Focus chain Y [auth D] Interactions & Density Focus chain BA [auth E] Focus chain EA [auth F] Focus chain HA [auth G] Focus chain P [auth A] Focus chain S [auth B] Focus chain V [auth C] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.95 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	Spain	--