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- PDB-9vm4: Structure of DOCK6-Rac1 complex protomer -

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Basic information

Entry
Database: PDB / ID: 9vm4
TitleStructure of DOCK6-Rac1 complex protomer
Components
  • Dedicator of cytokinesis protein 6
  • Ras-related C3 botulinum toxin substrate 1
KeywordsSIGNALING PROTEIN / DOCK / GEF / Rho / small GTPase / Rac / Cdc42
Function / homology
Function and homology information


regulation of respiratory burst / positive regulation of ovarian follicle development / regulation of neutrophil migration / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / negative regulation of fibroblast migration / ruffle assembly / localization within membrane / kinocilium / regulation of cell adhesion involved in heart morphogenesis ...regulation of respiratory burst / positive regulation of ovarian follicle development / regulation of neutrophil migration / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / negative regulation of fibroblast migration / ruffle assembly / localization within membrane / kinocilium / regulation of cell adhesion involved in heart morphogenesis / NTRK2 activates RAC1 / NADPH oxidase complex / Inactivation of CDC42 and RAC1 / regulation of hydrogen peroxide metabolic process / Rac protein signal transduction / engulfment of apoptotic cell / superoxide anion generation / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / respiratory burst / motor neuron axon guidance / ruffle organization / positive regulation of bicellular tight junction assembly / GTP-dependent protein binding / regulation of Rho protein signal transduction / midbrain dopaminergic neuron differentiation / regulation of lamellipodium assembly / thioesterase binding / regulation of stress fiber assembly / RHO GTPases activate CIT / regulation of nitric oxide biosynthetic process / Nef and signal transduction / Activation of RAC1 / PCP/CE pathway / hepatocyte growth factor receptor signaling pathway / RHO GTPases activate KTN1 / forebrain development / sphingosine-1-phosphate receptor signaling pathway / DCC mediated attractive signaling / MET activates RAP1 and RAC1 / Sema4D mediated inhibition of cell attachment and migration / Azathioprine ADME / lamellipodium assembly / CD28 dependent Vav1 pathway / Ephrin signaling / positive regulation of neutrophil chemotaxis / Wnt signaling pathway, planar cell polarity pathway / positive regulation of ruffle assembly / regulation of receptor signaling pathway via JAK-STAT / NRAGE signals death through JNK / Rho GDP-dissociation inhibitor binding / small GTPase-mediated signal transduction / Activation of RAC1 downstream of NMDARs / positive regulation of Rho protein signal transduction / pericentriolar material / establishment or maintenance of cell polarity / CDC42 GTPase cycle / semaphorin-plexin signaling pathway / RHO GTPases activate PAKs / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / regulation of postsynapse assembly / ficolin-1-rich granule membrane / positive regulation of focal adhesion assembly / RHO GTPases Activate NADPH Oxidases / positive regulation of substrate adhesion-dependent cell spreading / anatomical structure morphogenesis / positive regulation of stress fiber assembly / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / substrate adhesion-dependent cell spreading / positive regulation of lamellipodium assembly / cell-matrix adhesion / RHO GTPases activate IQGAPs / GPVI-mediated activation cascade / RHO GTPases activate PKNs / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / phagocytic cup / actin filament polymerization / RAC1 GTPase cycle / EPHB-mediated forward signaling / regulation of cell migration / positive regulation of endothelial cell migration / guanyl-nucleotide exchange factor activity / actin filament organization / cell motility / secretory granule membrane / Signal transduction by L1 / positive regulation of insulin secretion involved in cellular response to glucose stimulus / VEGFR2 mediated vascular permeability / small monomeric GTPase / FCGR3A-mediated phagocytosis / cell chemotaxis / FCERI mediated MAPK activation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / response to wounding / trans-Golgi network / SRC activates STAT3 in a quantitative manner, through Cadherin-11 (CDH11), RAC1 and gp130 (IL6ST) / neuron migration / regulation of cell shape
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. / Small GTPase Rho / Small GTPase Rho domain profile. / C2 domain superfamily / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Ras-related C3 botulinum toxin substrate 1 / Dedicator of cytokinesis protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 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
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dedicator of cytokinesis protein 6
B: Ras-related C3 botulinum toxin substrate 1


Theoretical massNumber of molelcules
Total (without water)250,5102
Polymers250,5102
Non-polymers00
Water00
1


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

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Components

#1: Protein Dedicator of cytokinesis protein 6


Mass: 230265.312 Da / Num. of mol.: 1
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
#2: Protein Ras-related C3 botulinum toxin substrate 1 / Cell migration-inducing gene 5 protein / Ras-like protein TC25 / p21-Rac1


Mass: 20244.258 Da / Num. of mol.: 1 / Mutation: G15A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1, TC25, MIG5 / Production host: Escherichia coli (E. coli) / References: UniProt: P63000, small monomeric GTPase
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Binary complex of DOCK6 with Rac1 / 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

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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: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 49.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 5048

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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: 21977481
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 313646 / Num. of class averages: 2 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00815202
ELECTRON MICROSCOPYf_angle_d0.92720632
ELECTRON MICROSCOPYf_dihedral_angle_d6.8012034
ELECTRON MICROSCOPYf_chiral_restr0.052329
ELECTRON MICROSCOPYf_plane_restr0.0062672

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