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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 / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / dendritic cell migration / neuron fate determination / apolipoprotein A-I receptor binding / positive regulation of epithelial cell proliferation involved in lung morphogenesis ...GBD domain binding / positive regulation of pinocytosis / COG complex / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / dendritic cell migration / neuron fate determination / apolipoprotein A-I receptor binding / positive regulation of epithelial cell proliferation involved in lung morphogenesis / regulation of attachment of spindle microtubules to kinetochore / organelle transport along microtubule / positive regulation of pseudopodium assembly / Inactivation of CDC42 and RAC1 / host-mediated perturbation of viral process / cardiac conduction system development / leading edge membrane / neuropilin signaling pathway / regulation of filopodium assembly / establishment of Golgi localization / filopodium assembly / cell junction assembly / establishment of epithelial cell apical/basal polarity / dendritic spine morphogenesis / adherens junction organization / GTP-dependent protein binding / regulation of Rho protein signal transduction / thioesterase binding / regulation of lamellipodium assembly / regulation of stress fiber assembly / embryonic heart tube development / RHO GTPases activate KTN1 / DCC mediated attractive signaling / CD28 dependent Vav1 pathway / regulation of postsynapse organization / positive regulation of filopodium assembly / Wnt signaling pathway, planar cell polarity pathway / phagocytosis, engulfment / RHOV GTPase cycle / regulation of mitotic nuclear division / Myogenesis / nuclear migration / small GTPase-mediated signal transduction / positive regulation of cytokinesis / spindle midzone / RHOJ GTPase cycle / heart contraction / RHOQ GTPase cycle / establishment of cell polarity / Golgi organization / RHOU GTPase cycle / establishment or maintenance of cell polarity / RHO GTPases activate PAKs / CDC42 GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / negative regulation of protein-containing complex assembly / RHO GTPases activate IQGAPs / GPVI-mediated activation cascade / positive regulation of lamellipodium assembly / phagocytic vesicle / positive regulation of stress fiber assembly / RAC1 GTPase cycle / EPHB-mediated forward signaling / positive regulation of substrate adhesion-dependent cell spreading / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / guanyl-nucleotide exchange factor activity / integrin-mediated signaling pathway / actin filament organization / small monomeric GTPase / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / filopodium / EGFR downregulation / RHO GTPases Activate Formins / Regulation of actin dynamics for phagocytic cup formation / MAPK6/MAPK4 signaling / VEGFA-VEGFR2 Pathway / cellular response to type II interferon / endocytosis / apical part of cell / cytoplasmic ribonucleoprotein granule / cell-cell junction / mitotic spindle / G beta:gamma signalling through CDC42 / intracellular protein localization / ubiquitin protein ligase activity / Factors involved in megakaryocyte development and platelet production / positive regulation of cell growth / actin cytoskeleton organization / G protein activity / midbody / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / neuron projection / postsynapse
Similarity search - Function
Dedicator of cytokinesis C, C2 domain / Dedicator of cytokinesis C/D, N-terminal / Dedicator of cytokinesis C/D, N terminal / 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 ...Dedicator of cytokinesis C, C2 domain / Dedicator of cytokinesis C/D, N-terminal / Dedicator of cytokinesis C/D, N terminal / 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: To Be Published
Title: Structural basis for auto-inhibition of the Rac1/Cdc42 guanine nucleotide exchange factor DOCK6 by oligomer formation
Authors: Kukimoto-Niino, M. / Katsura, K. / Yoshimura, K. / Ishizuka-Katsura, Y. / Miyamoto, Y. / Yonemochi, M. / Hanada, K. / Yamauchi, J. / Wong, R.W. / Shirouzu, M.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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