9ES6 | pdb_00009es6

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


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 1.1 of the entry. See complete history


Literature

Structural basis for ATP-driven double-ring assembly of the human mitochondrial Hsp60 chaperonin.

Tascon, I.Lopez-Alonso, J.P.Shkolnisky, Y.Gil-Carton, D.Vilchez-Garcia, J.Berruezo, A.G.Gomez-Llorente, Y.Malik, R.Jebara, F.Patra, M.Hirsch, J.A.Azem, A.Ubarretxena-Belandia, I.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2025.10.04.680452
  • Primary Citation of Related Structures:  
    9ES0, 9ES1, 9ES2, 9ES3, 9ES4, 9ES5, 9ES6, 9H5S, 9H5T, 9H5U, 9H5V

  • PubMed Abstract: 

    The ATP-driven mHsp60:mHsp10 chaperonin system assists protein folding within the mitochondrial matrix of human cells. Substrate protein folding has been proposed to occur through interconnected single- and double-ring pathways. In the absence of nucleotide, mHsp60 exists in equilibrium between free protomers and heptameric single rings, while the formation of double rings requires ATP. Here, we present cryo-electron microscopy structures of mHsp60 in the apo state, bound to ATP, and bound to ATP in complex with the cochaperonin mHsp10. ATP binding to single-ring apo mHsp60 7 triggers coordinated conformational changes in the intermediate and apical domains, resulting in a highly dynamic apical region within the ring. Extensive inter-subunit rearrangements flatten the equatorial surface of each ring, thereby enabling inter-ring contacts that stitch the rings together to form double-ring mHsp60 14 . Collectively, these structures define the structural basis of ATP-driven double-ring assembly of a human mitochondrial chaperonin responsible for maintaining mitochondrial protein homeostasis.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
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
549Homo sapiensMutation(s): 0 
Gene Names: HSPD1HSP60
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10809
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
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
BEF (Subject of Investigation/LOI)
Query on BEF

Download Ideal Coordinates CCD File 
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
K
Query on K

Download Ideal Coordinates CCD File 
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
MG
Query on MG

Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United States - Israel Binational Science Foundation (BSF)United States--
Spanish Ministry of Science, Innovation, and UniversitiesSpain--
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Data collection, Database references