9VM5 | pdb_00009vm5

Structure of DOCK6-Rac1 complex

• PDB DOI: https://doi.org/10.2210/pdb9VM5/pdb
• EM Map EMD-65177: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-06-27 Released: 2026-06-03 
• Deposition Author(s): Kukimoto-Niino, M., Katsura, K., Ishizuka-Katsura, Y., Yonemochi, M., Hanada, K., Shirouzu, M.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 5.32 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for auto-inhibition of the Rac1/Cdc42 guanine nucleotide exchange factor DOCK6 by oligomer formation

Kukimoto-Niino, M., Katsura, K., Yoshimura, K., Ishizuka-Katsura, Y., Miyamoto, Y., Yonemochi, M., Hanada, K., Yamauchi, J., Wong, R.W., Shirouzu, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 501.02 kDa 
• Atom Count: 29,712 
• Modeled Residue Count: 3,730 
• Deposited Residue Count: 4,474 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dedicator of cytokinesis protein 6	A, C	2,053	Homo sapiens	Mutation(s): 0  Gene Names: DOCK6, KIAA1395
UniProt & NIH Common Fund Data Resources
Find proteins for Q96HP0 (Homo sapiens) Explore Q96HP0  Go to UniProtKB:  Q96HP0
PHAROS:  Q96HP0 GTEx:  ENSG00000130158

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related C3 botulinum toxin substrate 1	B, D	184	Homo sapiens	Mutation(s): 1  Gene Names: RAC1, TC25, MIG5 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P63000 (Homo sapiens) Explore P63000  Go to UniProtKB:  P63000
PHAROS:  P63000 GTEx:  ENSG00000136238

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 5.32 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.18.2_3874
RECONSTRUCTION	RELION	3.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-03 
Deposition Author(s): Kukimoto-Niino, M., Katsura, K., Ishizuka-Katsura, Y., Yonemochi, M., Hanada, K., Shirouzu, M.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP15K06987
Japan Society for the Promotion of Science (JSPS)	Japan	JP22H05551
Japan Society for the Promotion of Science (JSPS)	Japan	JP25K02219
Japan Science and Technology	Japan	JPMJCR22E3

Revision History  

• Version 1.0: 2026-06-03
  Type: Initial release