9VM6 | pdb_00009vm6

Structure of DOCK6 tetramer

PDB DOI: https://doi.org/10.2210/pdb9VM6/pdb
EM Map EMD-65178: EMDB EMDataResource

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

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

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.27 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9VM6

This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 921.06 kDa
Atom Count: 53,700
Modeled Residue Count: 6,732
Deposited Residue Count: 8,212
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dedicator of cytokinesis protein 6	A, B [auth C], C [auth D], D [auth B]	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96HP0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.27 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

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-03

Deposition Author(s):

Kukimoto-Niino, M.

Ishizuka-Katsura, Y.

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 (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.