9ES6 | pdb_00009es6

ADP:BeF3-bound human mitochondrial Hsp60 double-ring complex

PDB DOI: https://doi.org/10.2210/pdb9ES6/pdb
EM Map EMD-19936: 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., Shkolnisky, Y.
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: 3.00 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 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: 822.3 kDa
Atom Count: 35,308
Modeled Residue Count: 4,746
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 4 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 AA [auth D] SDF format, chain CB [auth K] SDF format, chain EA [auth E] SDF format, chain GB [auth L] SDF format, chain IA [auth F] SDF format, chain KB [auth M] SDF format, chain MA [auth G] SDF format, chain O [auth A] SDF format, chain OB [auth N] SDF format, chain S [auth B] SDF format, chain UA [auth I] SDF format, chain W [auth C] SDF format, chain YA [auth J] SDF format, chain QA [auth H] MOL2 format, chain AA [auth D] MOL2 format, chain CB [auth K] MOL2 format, chain EA [auth E] MOL2 format, chain GB [auth L] MOL2 format, chain IA [auth F] MOL2 format, chain KB [auth M] MOL2 format, chain MA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain OB [auth N] MOL2 format, chain S [auth B] MOL2 format, chain UA [auth I] MOL2 format, chain W [auth C] MOL2 format, chain YA [auth J] MOL2 format, chain QA [auth H] mmCIF format, chain AA [auth D] mmCIF format, chain CB [auth K] mmCIF format, chain EA [auth E] mmCIF format, chain GB [auth L] mmCIF format, chain IA [auth F] mmCIF format, chain KB [auth M] mmCIF format, chain MA [auth G] mmCIF format, chain O [auth A] mmCIF format, chain OB [auth N] mmCIF format, chain S [auth B] mmCIF format, chain UA [auth I] mmCIF format, chain W [auth C] mmCIF format, chain YA [auth J] mmCIF format, chain QA [auth H]	AA [auth D] CB [auth K] EA [auth E] GB [auth L] IA [auth F] AA [auth D], CB [auth K], EA [auth E], GB [auth L], IA [auth F], KB [auth M], MA [auth G], O [auth A], OB [auth N], QA [auth H], S [auth B], UA [auth I], W [auth C], YA [auth J]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth D] Focus chain CB [auth K] Focus chain EA [auth E] Focus chain GB [auth L] Focus chain IA [auth F] Focus chain KB [auth M] Focus chain MA [auth G] Focus chain O [auth A] Focus chain OB [auth N] Focus chain QA [auth H] Focus chain S [auth B] Focus chain UA [auth I] Focus chain W [auth C] Focus chain YA [auth J] Interactions & Density Focus chain AA [auth D] Focus chain CB [auth K] Focus chain EA [auth E] Focus chain GB [auth L] Focus chain IA [auth F] Focus chain KB [auth M] Focus chain MA [auth G] Focus chain O [auth A] Focus chain OB [auth N] Focus chain QA [auth H] Focus chain S [auth B] Focus chain UA [auth I] Focus chain W [auth C] Focus chain YA [auth J]
BEF (Subject of Investigation/LOI) Query on BEF Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain DB [auth K] SDF format, chain FA [auth E] SDF format, chain HB [auth L] SDF format, chain JA [auth F] SDF format, chain LB [auth M] SDF format, chain NA [auth G] SDF format, chain P [auth A] SDF format, chain PB [auth N] SDF format, chain RA [auth H] SDF format, chain T [auth B] SDF format, chain VA [auth I] SDF format, chain X [auth C] SDF format, chain ZA [auth J] MOL2 format, chain BA [auth D] MOL2 format, chain DB [auth K] MOL2 format, chain FA [auth E] MOL2 format, chain HB [auth L] MOL2 format, chain JA [auth F] MOL2 format, chain LB [auth M] MOL2 format, chain NA [auth G] MOL2 format, chain P [auth A] MOL2 format, chain PB [auth N] MOL2 format, chain RA [auth H] MOL2 format, chain T [auth B] MOL2 format, chain VA [auth I] MOL2 format, chain X [auth C] MOL2 format, chain ZA [auth J] mmCIF format, chain BA [auth D] mmCIF format, chain DB [auth K] mmCIF format, chain FA [auth E] mmCIF format, chain HB [auth L] mmCIF format, chain JA [auth F] mmCIF format, chain LB [auth M] mmCIF format, chain NA [auth G] mmCIF format, chain P [auth A] mmCIF format, chain PB [auth N] mmCIF format, chain RA [auth H] mmCIF format, chain T [auth B] mmCIF format, chain VA [auth I] mmCIF format, chain X [auth C] mmCIF format, chain ZA [auth J]	BA [auth D] DB [auth K] FA [auth E] HB [auth L] JA [auth F] BA [auth D], DB [auth K], FA [auth E], HB [auth L], JA [auth F], LB [auth M], NA [auth G], P [auth A], PB [auth N], RA [auth H], T [auth B], VA [auth I], X [auth C], ZA [auth J]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain BA [auth D] Focus chain DB [auth K] Focus chain FA [auth E] Focus chain HB [auth L] Focus chain JA [auth F] Focus chain LB [auth M] Focus chain NA [auth G] Focus chain P [auth A] Focus chain PB [auth N] Focus chain RA [auth H] Focus chain T [auth B] Focus chain VA [auth I] Focus chain X [auth C] Focus chain ZA [auth J] Interactions & Density Focus chain BA [auth D] Focus chain DB [auth K] Focus chain FA [auth E] Focus chain HB [auth L] Focus chain JA [auth F] Focus chain LB [auth M] Focus chain NA [auth G] Focus chain P [auth A] Focus chain PB [auth N] Focus chain RA [auth H] Focus chain T [auth B] Focus chain VA [auth I] Focus chain X [auth C] Focus chain ZA [auth J]
K Query on K Download Ideal Coordinates CCD File SDF format, chain BB [auth J] SDF format, chain DA [auth D] SDF format, chain FB [auth K] SDF format, chain HA [auth E] SDF format, chain JB [auth L] SDF format, chain LA [auth F] SDF format, chain NB [auth M] SDF format, chain PA [auth G] SDF format, chain R [auth A] SDF format, chain RB [auth N] SDF format, chain TA [auth H] SDF format, chain V [auth B] SDF format, chain XA [auth I] SDF format, chain Z [auth C] MOL2 format, chain BB [auth J] MOL2 format, chain DA [auth D] MOL2 format, chain FB [auth K] MOL2 format, chain HA [auth E] MOL2 format, chain JB [auth L] MOL2 format, chain LA [auth F] MOL2 format, chain NB [auth M] MOL2 format, chain PA [auth G] MOL2 format, chain R [auth A] MOL2 format, chain RB [auth N] MOL2 format, chain TA [auth H] MOL2 format, chain V [auth B] MOL2 format, chain XA [auth I] MOL2 format, chain Z [auth C] mmCIF format, chain BB [auth J] mmCIF format, chain DA [auth D] mmCIF format, chain FB [auth K] mmCIF format, chain HA [auth E] mmCIF format, chain JB [auth L] mmCIF format, chain LA [auth F] mmCIF format, chain NB [auth M] mmCIF format, chain PA [auth G] mmCIF format, chain R [auth A] mmCIF format, chain RB [auth N] mmCIF format, chain TA [auth H] mmCIF format, chain V [auth B] mmCIF format, chain XA [auth I] mmCIF format, chain Z [auth C]	BB [auth J] DA [auth D] FB [auth K] HA [auth E] JB [auth L] BB [auth J], DA [auth D], FB [auth K], HA [auth E], JB [auth L], LA [auth F], NB [auth M], PA [auth G], R [auth A], RB [auth N], TA [auth H], V [auth B], XA [auth I], Z [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain BB [auth J] Focus chain DA [auth D] Focus chain FB [auth K] Focus chain HA [auth E] Focus chain JB [auth L] Focus chain LA [auth F] Focus chain NB [auth M] Focus chain PA [auth G] Focus chain R [auth A] Focus chain RB [auth N] Focus chain TA [auth H] Focus chain V [auth B] Focus chain XA [auth I] Focus chain Z [auth C] Interactions & Density Focus chain BB [auth J] Focus chain DA [auth D] Focus chain FB [auth K] Focus chain HA [auth E] Focus chain JB [auth L] Focus chain LA [auth F] Focus chain NB [auth M] Focus chain PA [auth G] Focus chain R [auth A] Focus chain RB [auth N] Focus chain TA [auth H] Focus chain V [auth B] Focus chain XA [auth I] Focus chain Z [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AB [auth J] SDF format, chain CA [auth D] SDF format, chain EB [auth K] SDF format, chain GA [auth E] SDF format, chain IB [auth L] SDF format, chain KA [auth F] SDF format, chain MB [auth M] SDF format, chain OA [auth G] SDF format, chain Q [auth A] SDF format, chain QB [auth N] SDF format, chain SA [auth H] SDF format, chain U [auth B] SDF format, chain WA [auth I] SDF format, chain Y [auth C] MOL2 format, chain AB [auth J] MOL2 format, chain CA [auth D] MOL2 format, chain EB [auth K] MOL2 format, chain GA [auth E] MOL2 format, chain IB [auth L] MOL2 format, chain KA [auth F] MOL2 format, chain MB [auth M] MOL2 format, chain OA [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain QB [auth N] MOL2 format, chain SA [auth H] MOL2 format, chain U [auth B] MOL2 format, chain WA [auth I] MOL2 format, chain Y [auth C] mmCIF format, chain AB [auth J] mmCIF format, chain CA [auth D] mmCIF format, chain EB [auth K] mmCIF format, chain GA [auth E] mmCIF format, chain IB [auth L] mmCIF format, chain KA [auth F] mmCIF format, chain MB [auth M] mmCIF format, chain OA [auth G] mmCIF format, chain Q [auth A] mmCIF format, chain QB [auth N] mmCIF format, chain SA [auth H] mmCIF format, chain U [auth B] mmCIF format, chain WA [auth I] mmCIF format, chain Y [auth C]	AB [auth J] CA [auth D] EB [auth K] GA [auth E] IB [auth L] AB [auth J], CA [auth D], EB [auth K], GA [auth E], IB [auth L], KA [auth F], MB [auth M], OA [auth G], Q [auth A], QB [auth N], SA [auth H], U [auth B], WA [auth I], Y [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth J] Focus chain CA [auth D] Focus chain EB [auth K] Focus chain GA [auth E] Focus chain IB [auth L] Focus chain KA [auth F] Focus chain MB [auth M] Focus chain OA [auth G] Focus chain Q [auth A] Focus chain QB [auth N] Focus chain SA [auth H] Focus chain U [auth B] Focus chain WA [auth I] Focus chain Y [auth C] Interactions & Density Focus chain AB [auth J] Focus chain CA [auth D] Focus chain EB [auth K] Focus chain GA [auth E] Focus chain IB [auth L] Focus chain KA [auth F] Focus chain MB [auth M] Focus chain OA [auth G] Focus chain Q [auth A] Focus chain QB [auth N] Focus chain SA [auth H] Focus chain U [auth B] Focus chain WA [auth I] Focus chain Y [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0

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.

Shkolnisky, Y.

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