9H5S | pdb_00009h5s

ATP-bound human mitochondrial Hsp60-Hsp10 football complex (C1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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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, mitochondrial549Homo 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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
10 kDa heat shock protein, mitochondrial102Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61604
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
AB [auth I]
CA [auth A]
DB [auth J]
FA [auth B]
GB [auth K]
AB [auth I],
CA [auth A],
DB [auth J],
FA [auth B],
GB [auth K],
IA [auth C],
JB [auth L],
LA [auth D],
MB [auth M],
OA [auth E],
PB [auth N],
RA [auth F],
UA [auth G],
XA [auth H]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
K
Query on K

Download Ideal Coordinates CCD File 
CB [auth I]
EA [auth A]
FB [auth J]
HA [auth B]
IB [auth K]
CB [auth I],
EA [auth A],
FB [auth J],
HA [auth B],
IB [auth K],
KA [auth C],
LB [auth L],
NA [auth D],
OB [auth M],
QA [auth E],
RB [auth N],
TA [auth F],
WA [auth G],
ZA [auth H]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BB [auth I]
DA [auth A]
EB [auth J]
GA [auth B]
HB [auth K]
BB [auth I],
DA [auth A],
EB [auth J],
GA [auth B],
HB [auth K],
JA [auth C],
KB [auth L],
MA [auth D],
NB [auth M],
PA [auth E],
QB [auth N],
SA [auth F],
VA [auth G],
YA [auth H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21rc1_4933

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: 2025-11-05
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Data collection, Database references