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- EMDB-65174: Structure of DOCK6-Cdc42 complex protomer -

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Basic information

Entry
Database: EMDB / ID: EMD-65174
TitleStructure of DOCK6-Cdc42 complex protomer
Map datapostprocess map
Sample
  • Complex: Binary complex of DOCK6 with Cdc42
    • Protein or peptide: Dedicator of cytokinesis protein 6
    • Protein or peptide: Cell division control protein 42 homolog
KeywordsDOCK / GEF / Rho / small GTPase / Rac / Cdc42 / SIGNALING PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsKukimoto-Niino M / Katsura K / Ishizuka-Katsura Y / Yonemochi M / Hanada K / Shirouzu M
Funding support Japan, 4 items
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, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65174.png

Downloads & links

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Map

FileDownload / File: emd_65174.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpostprocess map
Projections & slices

Image control

Size
Brightness
Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 240 pix.
= 319.2 Å		1.33 Å/pix.
x 240 pix.
= 319.2 Å		1.33 Å/pix.
x 240 pix.
= 319.2 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.33 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.0992128 - 0.18498442
Average (Standard dev.)-0.000131011 (±0.0043347785)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 319.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half1 map

Fileemd_65174_half_map_1.map
Annotationhalf1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half2 map

Fileemd_65174_half_map_2.map
Annotationhalf2 map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Binary complex of DOCK6 with Cdc42

EntireName: Binary complex of DOCK6 with Cdc42
Components
  • Complex: Binary complex of DOCK6 with Cdc42
    • Protein or peptide: Dedicator of cytokinesis protein 6
    • Protein or peptide: Cell division control protein 42 homolog

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Supramolecule #1: Binary complex of DOCK6 with Cdc42

SupramoleculeName: Binary complex of DOCK6 with Cdc42 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Dedicator of cytokinesis protein 6

MacromoleculeName: Dedicator of cytokinesis protein 6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 230.265312 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GGSGGSMAAS ERRAFAHKIN RTVAAEVRKQ VSRERSGSPH SSRRCSSSLG VPLTEVVEPL DFEDVLLSRP PDAEPGPLRD LVEFPADDL ELLLQPRECR TTEPGIPKDE KLDAQVRAAV EMYIEDWVIV HRRYQYLSAA YSPVTTDTQR ERQKGLPRQV F EQDASGDE ...String:
GGSGGSMAAS ERRAFAHKIN RTVAAEVRKQ VSRERSGSPH SSRRCSSSLG VPLTEVVEPL DFEDVLLSRP PDAEPGPLRD LVEFPADDL ELLLQPRECR TTEPGIPKDE KLDAQVRAAV EMYIEDWVIV HRRYQYLSAA YSPVTTDTQR ERQKGLPRQV F EQDASGDE RSGPEDSNDS RRGSGSPEDT PRSSGASSIF DLRNLAADSL LPSLLERAAP EDVDRRNETL RRQHRPPALL TL YPAPDED EAVERCSRPE PPREHFGQRI LVKCLSLKFE IEIEPIFGIL ALYDVREKKK ISENFYFDLN SDSMKGLLRA HGT HPAIST LARSAIFSVT YPSPDIFLVI KLEKVLQQGD ISECCEPYMV LKEVDTAKNK EKLEKLRLAA EQFCTRLGRY RMPF AWTAV HLANIVSSAG QLDRDSDSEG ERRPAWTDRR RRGPQDRASS GDDACSFSGF RPATLTVTNF FKQEAERLSD EDLFK FLAD MRRPSSLLRR LRPVTAQLKI DISPAPENPH FCLSPELLHI KPYPDPRGRP TKEILEFPAR EVYAPHTSYR NLLYVY PHS LNFSSRQGSV RNLAVRVQYM TGEDPSQALP VIFGKSSCSE FTREAFTPVV YHNKSPEFYE EFKLHLPACV TENHHLL FT FYHVSCQPRP GTALETPVGF TWIPLLQHGR LRTGPFCLPV SVDQPPPSYS VLTPDVALPG MRWVDGHKGV FSVELTAV S SVHPQDPYLD KFFTLVHVLE EGAFPFRLKD TVLSEGNVEQ ELRASLAALR LASPEPLVAF SHHVLDKLVR LVIRPPIIS GQIVNLGRGA FEAMAHVVSL VHRSLEAAQD ARGHCPQLAA YVHYAFRLPG TEPSLPDGAP PVTVQAATLA RGSGRPASLY LARSKSISS SNPDLAVAPG SVDDEVSRIL ASKLLHEELA LQWVVSSSAV REAILQHAWF FFQLMVKSMA LHLLLGQRLD T PRKLRFPG RFLDDITALV GSVGLEVITR VHKDVELAEH LNASLAFFLS DLLSLVDRGF VFSLVRAHYK QVATRLQSSP NP AALLTLR MEFTRILCSH EHYVTLNLPC CPLSPPASPS PSVSSTTSQS STFSSQAPDP KVTSMFELSG PFRQQHFLAG LLL TELALA LEPEAEGAFL LHKKAISAVH SLLCGHDTDP RYAEATVKAR VAELYLPLLS IARDTLPRLH DFAEGPGQRS RLAS MLDSD TEGEGDIAGT INPSVAMAIA GGPLAPGSRA SISQGPPTAS RAGCALSAES SRTLLACVLW VLKNTEPALL QRWAT DLTL PQLGRLLDLL YLCLAAFEYK GKKAFERINS LTFKKSLDMK ARLEEAILGT IGARQEMVRR SRERSPFGNP ENVRWR KSV THWKQTSDRV DKTKDEMEHE ALVEGNLATE ASLVVLDTLE IIVQTVMLSE ARESVLGAVL KVVLYSLGSA QSALFLQ HG LATQRALVSK FPELLFEEDT ELCADLCLRL LRHCGSRIST IRTHASASLY LLMRQNFEIG HNFARVKMQV TMSLSSLV G TTQNFSEEHL RRSLKTILTY AEEDMGLRDS TFAEQVQDLM FNLHMILTDT VKMKEHQEDP EMLIDLMYRI ARGYQGSPD LRLTWLQNMA GKHAELGNHA EAAQCMVHAA ALVAEYLALL EDHRHLPVGC VSFQNISSNV LEESAISDDI LSPDEEGFCS GKHFTELGL VGLLEQAAGY FTMGGLYEAV NEVYKNLIPI LEAHRDYKKL AAVHGKLQEA FTKIMHQSSG WERVFGTYFR V GFYGAHFG DLDEQEFVYK EPSITKLAEI SHRLEEFYTE RFGDDVVEII KDSNPVDKSK LDSQKAYIQI TYVEPYFDTY EL KDRVTYF DRNYGLRTFL FCTPFTPDGR AHGELPEQHK RKTLLSTDHA FPYIKTRIRV CHREETVLTP VEVAIEDMQK KTR ELAFAT EQDPPDAKML QMVLQGSVGP TVNQGPLEVA QVFLAEIPED PKLFRHHNKL RLCFKDFCKK CEDALRKNKA LIGP DQKEY HRELERNYCR LREALQPLLT QRLPQLMAPT PPGLRNSLNR ASFRKADL

UniProtKB: Dedicator of cytokinesis protein 6

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Macromolecule #2: Cell division control protein 42 homolog

MacromoleculeName: Cell division control protein 42 homolog / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: small monomeric GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.475562 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSSGSSGMQT IKCVVVGDGA VAKTCLLISY TTNKFPSEYV PTVFDNYAVT VMIGGEPYTL GLFDTAGQED YDRLRPLSYP QTDVFLVCF SVVSPSSFEN VKEKWVPEIT HHCPKTPFLL VGTQIDLRDD PSTIEKLAKN KQKPITPETA EKLARDLKAV K YVECSALT ...String:
GSSGSSGMQT IKCVVVGDGA VAKTCLLISY TTNKFPSEYV PTVFDNYAVT VMIGGEPYTL GLFDTAGQED YDRLRPLSYP QTDVFLVCF SVVSPSSFEN VKEKWVPEIT HHCPKTPFLL VGTQIDLRDD PSTIEKLAKN KQKPITPETA EKLARDLKAV K YVECSALT QKGLKNVFDE AILAALEPPE PKKSRRS

UniProtKB: Cell division control protein 42 homolog

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 3377 / Average electron dose: 48.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 64000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1936198
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 259012
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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