9X4X | pdb_00009x4x

Cryo-EM structure of HSP90-CDC37-PINK1 complex

• PDB DOI: https://doi.org/10.2210/pdb9X4X/pdb
• EM Map EMD-66567: EMDB EMDataResource

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2025-10-12 Released: 2026-10-14 
• Deposition Author(s): Okatsu, K., Fukai, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.08 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for the folding of PINK1 by the HSP90-CDC37 chaperone complex

Okatsu, K., Yamamoto, H., Okamoto, A., Nishimoto, Y., Fukai, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 265.51 kDa 
• Atom Count: 14,094 
• Modeled Residue Count: 1,732 
• Deposited Residue Count: 2,312 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hsp90 co-chaperone Cdc37	A [auth C]	378	Homo sapiens	Mutation(s): 0  Gene Names: CDC37, CDC37A
UniProt & NIH Common Fund Data Resources
Find proteins for Q16543 (Homo sapiens) Explore Q16543  Go to UniProtKB:  Q16543
PHAROS:  Q16543 GTEx:  ENSG00000105401

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PINK1, mitochondrial	B [auth D]	486	Homo sapiens	Mutation(s): 1  Gene Names: PINK1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXM7 (Homo sapiens) Explore Q9BXM7  Go to UniProtKB:  Q9BXM7
PHAROS:  Q9BXM7 GTEx:  ENSG00000158828

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein HSP 90-beta	C [auth A], D [auth B]	724	Homo sapiens	Mutation(s): 0  Gene Names: HSP90AB1, HSP90B, HSPC2, HSPC3, HSPCB
UniProt & NIH Common Fund Data Resources
Find proteins for P08238 (Homo sapiens) Explore P08238  Go to UniProtKB:  P08238
PHAROS:  P08238 GTEx:  ENSG00000096384

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	E [auth A], G [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	F [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A [auth C]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.08 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158
RECONSTRUCTION	cryoSPARC	4.7.0

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-14 
Deposition Author(s): Okatsu, K., Fukai, S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	21K15084
Japan Society for the Promotion of Science (JSPS)	Japan	24H01894
Japan Society for the Promotion of Science (JSPS)	Japan	18H05501

Revision History  

• Version 1.0: 2026-10-14
  Type: Initial release