9SHL | pdb_00009shl

ATP-bound human mitochondrial Hsp60 single-ring complex (C7)

PDB DOI: https://doi.org/10.2210/pdb9SHL/pdb
EM Map EMD-54903: EMDB EMDataResource

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

Deposited: 2025-08-27 Released: 2025-12-10
Deposition Author(s): Lopez-Alonso, J.P., Tascon, I., Ubarretxena-Belandia, I.
Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN)

Experimental Data Snapshot

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

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9SHL

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

Literature

Structural remodeling of the mitochondrial protein biogenesis machinery upon proteostatic stress

Ehses, K., Lopez-Alonso, J.P., Gonzalez, A., Tascon, I., Ubarretxena-Belandia, I., Fernandez-Busnadiego, R.

To be published.

Macromolecule Content

Total Structure Weight: 396.94 kDa
Atom Count: 28,015
Modeled Residue Count: 3,689
Deposited Residue Count: 3,689
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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	527	Homo sapiens	Mutation(s): 0 Gene Names: HSPD1, HSP60 EC: 5.6.1.7
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 Z [auth G] SDF format, chain W [auth F] SDF format, chain T [auth E] SDF format, chain Q [auth D] SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain Z [auth G] MOL2 format, chain W [auth F] MOL2 format, chain T [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain Z [auth G] mmCIF format, chain W [auth F] mmCIF format, chain T [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	H [auth A] K [auth B] N [auth C] Q [auth D] T [auth E] H [auth A], K [auth B], N [auth C], Q [auth D], T [auth E], W [auth F], Z [auth G]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain W [auth F] Focus chain Z [auth G] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain W [auth F] Focus chain Z [auth G]
K (Subject of Investigation/LOI) Query on K Download:Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain V [auth E] SDF format, chain S [auth D] SDF format, chain P [auth C] SDF format, chain M [auth B] SDF format, chain J [auth A] SDF format, chain BA [auth G] MOL2 format, chain Y [auth F] MOL2 format, chain V [auth E] MOL2 format, chain S [auth D] MOL2 format, chain P [auth C] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain BA [auth G] mmCIF format, chain Y [auth F] mmCIF format, chain V [auth E] mmCIF format, chain S [auth D] mmCIF format, chain P [auth C] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A] mmCIF format, chain BA [auth G]	BA [auth G] J [auth A] M [auth B] P [auth C] S [auth D] BA [auth G], J [auth A], M [auth B], P [auth C], S [auth D], V [auth E], Y [auth F]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F] Interactions & Density Focus chain BA [auth G] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain X [auth F] SDF format, chain U [auth E] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain AA [auth G] MOL2 format, chain X [auth F] MOL2 format, chain U [auth E] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain AA [auth G] mmCIF format, chain X [auth F] mmCIF format, chain U [auth E] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain AA [auth G]	AA [auth G] I [auth A] L [auth B] O [auth C] R [auth D] AA [auth G], I [auth A], L [auth B], O [auth C], R [auth D], U [auth E], X [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F] Interactions & Density Focus chain AA [auth G] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F]

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.1.2
MODEL REFINEMENT	PHENIX	1.21rc1_4933
MODEL REFINEMENT	Coot	0.9.2

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-10

Deposition Author(s):

Lopez-Alonso, J.P.

Ubarretxena-Belandia, I.

Funding Organization	Location	Grant Number
Ministerio de Ciencia e Innovacion (MCIN)	Spain	PID2022-143177NB-I00

Revision History (Full details and data files)

Version 1.0: 2025-12-10
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.