[English] 日本語
Yorodumi
- PDB-9vm8: Structure of DOCK6 octamer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9vm8
TitleStructure of DOCK6 octamer
ComponentsDedicator of cytokinesis protein 6
KeywordsSIGNALING PROTEIN / DOCK / GEF / Rho / small GTPase / Rac / Cdc42
Function / homology
Function and homology information


regulation of Rho protein signal transduction / small GTPase-mediated signal transduction / CDC42 GTPase cycle / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity / Factors involved in megakaryocyte development and platelet production / perinuclear region of cytoplasm / cytosol
Similarity search - Function
: / Dedicator of cytokinesis C, C2 domain / Dedicator of cytokinesis C/D, N-terminal / Dedicator of cytokinesis C/D, N terminal / DOCK6-11, TPR domain / Dedicator of cytokinesis / C2 DOCK-type domain / DOCKER domain / Dedicator of cytokinesis, C-terminal, lobe A / Dedicator of cytokinesis, C-terminal, lobe C ...: / Dedicator of cytokinesis C, C2 domain / Dedicator of cytokinesis C/D, N-terminal / Dedicator of cytokinesis C/D, N terminal / DOCK6-11, TPR domain / Dedicator of cytokinesis / C2 DOCK-type domain / DOCKER domain / Dedicator of cytokinesis, C-terminal, lobe A / Dedicator of cytokinesis, C-terminal, lobe C / DOCKER, Lobe A / DOCKER, Lobe B / DOCKER, Lobe C / DHR-2, Lobe A / C2 domain in Dock180 and Zizimin proteins / DHR-2, Lobe C / DHR-2, Lobe B / C2 DOCK-type domain profile. / DOCKER domain profile. / C2 domain superfamily
Similarity search - Domain/homology
Dedicator of cytokinesis protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.53 Å
AuthorsKukimoto-Niino, M. / Katsura, K. / Ishizuka-Katsura, Y. / Yonemochi, M. / Hanada, K. / Shirouzu, M.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP15K06987 Japan
Japan Society for the Promotion of Science (JSPS)JP22H05551 Japan
Japan Society for the Promotion of Science (JSPS)JP25K02219 Japan
Japan Science and TechnologyJPMJCR22E3 Japan
CitationJournal: Commun Biol / Year: 2026
Title: Structural basis for auto-inhibition of the Rac1/Cdc42 guanine nucleotide exchange factor DOCK6 by oligomer formation.
Authors: Mutsuko Kukimoto-Niino / Kazushige Katsura / Kota Yoshimura / Yoshiko Ishizuka-Katsura / Yuki Miyamoto / Mayumi Yonemochi / Kazuharu Hanada / Junji Yamauchi / Richard W Wong / Mikako Shirouzu /
Abstract: The guanine nucleotide exchange factor DOCK6 is important for neurite outgrowth, as well as cell migration and invasion, through the activation of Rac1 and Cdc42-members of the Rho family of GTPases ...The guanine nucleotide exchange factor DOCK6 is important for neurite outgrowth, as well as cell migration and invasion, through the activation of Rac1 and Cdc42-members of the Rho family of GTPases that regulate the actin cytoskeleton. However, the precise molecular mechanisms by which DOCK6 regulates the intracellular GTPase signaling remain unclear. Here, we present cryo-electron microscopy structures of DOCK6 alone and in complex with Rac1 and Cdc42. The DOCK6-Rac1 and DOCK6-Cdc42 complexes exhibit similar homodimeric structures, with local differences in the catalytic domain of DOCK6 owing to distinct interactions with Rac1 and Cdc42. In contrast, apo-DOCK6 exhibits a closed auto-inhibited conformation in tetrameric and octameric assemblies, with the catalytic and membrane-binding domains contacting each other between two DOCK6 dimers. High-speed atomic force microscopy reveals transitions among multiple oligomers in solution. Biochemical and cellular functional analyses demonstrate that the N-terminal region of DOCK6 plays an auto-inhibitory role, supporting the structural findings. Overall, we propose a mechanism by which DOCK6 activity is spatiotemporally regulated within cells through oligomerization. These findings provide a framework for future studies of DOCK-family GEFs and their broader roles in cell regulation and human disease.
History
DepositionJun 27, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.1Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.2Sep 9, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.2Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin / Data content type: EM metadata / EM metadata / EM metadata
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dedicator of cytokinesis protein 6
C: Dedicator of cytokinesis protein 6
D: Dedicator of cytokinesis protein 6
B: Dedicator of cytokinesis protein 6
E: Dedicator of cytokinesis protein 6
F: Dedicator of cytokinesis protein 6
G: Dedicator of cytokinesis protein 6
H: Dedicator of cytokinesis protein 6


Theoretical massNumber of molelcules
Total (without water)1,842,1228
Polymers1,842,1228
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein
Dedicator of cytokinesis protein 6


Mass: 230265.312 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DOCK6, KIAA1395 / Production host: Homo sapiens (human) / References: UniProt: Q96HP0
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: DOCK6 octamer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 4317

-
Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2PHENIX1.18.2_3874model refinement
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1793089
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 7.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102384 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005110140
ELECTRON MICROSCOPYf_angle_d
ELECTRON MICROSCOPYf_dihedral_angle_d6.72914716
ELECTRON MICROSCOPYf_chiral_restr0.0516816
ELECTRON MICROSCOPYf_plane_restr0.00619400

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more