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- PDB-9vm3: Structure of DOCK6-Cdc42 complex -

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Basic information

Entry
Database: PDB / ID: 9vm3
TitleStructure of DOCK6-Cdc42 complex
Components
  • Cell division control protein 42 homolog
  • Dedicator of cytokinesis protein 6
KeywordsSIGNALING PROTEIN / DOCK / GEF / Rho / small GTPase / Rac / Cdc42
Function / homology
Function and homology information


GBD domain binding / positive regulation of pinocytosis / COG complex / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / regulation of attachment of spindle microtubules to kinetochore / embryonic heart tube development / organelle transport along microtubule ...GBD domain binding / positive regulation of pinocytosis / COG complex / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / regulation of attachment of spindle microtubules to kinetochore / embryonic heart tube development / organelle transport along microtubule / endothelin receptor signaling pathway / Inactivation of CDC42 and RAC1 / positive regulation of pseudopodium assembly / host-mediated perturbation of viral process / leading edge membrane / regulation of filopodium assembly / neuropilin signaling pathway / establishment of Golgi localization / dendritic spine morphogenesis / establishment of epithelial cell apical/basal polarity / cell junction assembly / GTP-dependent protein binding / regulation of Rho protein signal transduction / heart process / regulation of lamellipodium assembly / thioesterase binding / regulation of stress fiber assembly / RHO GTPases activate KTN1 / DCC mediated attractive signaling / positive regulation of filopodium assembly / CD28 dependent Vav1 pathway / regulation of postsynapse organization / Wnt signaling pathway, planar cell polarity pathway / phagocytosis, engulfment / RHOV GTPase cycle / Myogenesis / establishment of cell polarity / small GTPase-mediated signal transduction / spindle midzone / positive regulation of cytokinesis / RHOJ GTPase cycle / RHOQ GTPase cycle / Golgi organization / RHOU GTPase cycle / macrophage differentiation / establishment or maintenance of cell polarity / CDC42 GTPase cycle / RHO GTPases activate PAKs / RHOG GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / RHO GTPases Activate WASPs and WAVEs / positive regulation of lamellipodium assembly / negative regulation of protein-containing complex assembly / RHO GTPases activate IQGAPs / GPVI-mediated activation cascade / RAC1 GTPase cycle / phagocytic vesicle / EPHB-mediated forward signaling / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / guanyl-nucleotide exchange factor activity / actin filament organization / integrin-mediated signaling pathway / acrosomal vesicle / regulation of actin cytoskeleton organization / small monomeric GTPase / FCGR3A-mediated phagocytosis / filopodium / SRC activates STAT3 in a quantitative manner, through Cadherin-11 (CDH11), RAC1 and gp130 (IL6ST) / endocytosis / EGFR downregulation / RHO GTPases Activate Formins / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / mitotic spindle / MAPK6/MAPK4 signaling / Activation of STAT3 by cadherin engagement / apical part of cell / cytoplasmic ribonucleoprotein granule / microtubule cytoskeleton / actin cytoskeleton organization / cell-cell junction / G beta:gamma signalling through CDC42 / ubiquitin protein ligase activity / positive regulation of cell growth / Factors involved in megakaryocyte development and platelet production / midbody / G protein activity / neuron projection / postsynapse / positive regulation of cell migration / Golgi membrane / focal adhesion / centrosome / neuronal cell body / GTPase activity / dendrite
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 / Cdc42 / Dedicator of cytokinesis / C2 DOCK-type domain / DOCKER domain / Dedicator of cytokinesis, C-terminal, lobe A ...: / Dedicator of cytokinesis C, C2 domain / Dedicator of cytokinesis C/D, N-terminal / Dedicator of cytokinesis C/D, N terminal / DOCK6-11, TPR domain / Cdc42 / 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
Cell division control protein 42 homolog / Dedicator of cytokinesis protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.52 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
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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: Cell division control protein 42 homolog
C: Dedicator of cytokinesis protein 6
D: Cell division control protein 42 homolog


Theoretical massNumber of molelcules
Total (without water)503,4824
Polymers503,4824
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.: 2
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 Cell division control protein 42 homolog / G25K GTP-binding protein


Mass: 21475.562 Da / Num. of mol.: 2 / Mutation: G15A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42 / Production host: Escherichia coli (E. coli) / References: UniProt: P60953, 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 Cdc42 / 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: 48.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 3377

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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: 1936198
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 370326 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00630412
ELECTRON MICROSCOPYf_angle_d0.88841276
ELECTRON MICROSCOPYf_dihedral_angle_d6.3434060
ELECTRON MICROSCOPYf_chiral_restr0.0474668
ELECTRON MICROSCOPYf_plane_restr0.0065344

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