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- EMDB-65179: Structure of DOCK6 tetramer complexed with Rac1 -

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Basic information

Entry
Database: EMDB / ID: EMD-65179
TitleStructure of DOCK6 tetramer complexed with Rac1
Map data
Sample
  • Complex: DOCK6 tetramer complexed with Rac1
    • Protein or peptide: Dedicator of cytokinesis protein 6
    • Protein or peptide: Ras-related C3 botulinum toxin substrate 1
KeywordsDOCK / GEF / Rho / small GTPase / Rac / Cdc42 / SIGNALING PROTEIN
Function / homology
Function and homology information


embryonic olfactory bulb interneuron precursor migration / anatomical structure arrangement / regulation of ERK5 cascade / angiotensin-activated signaling pathway involved in heart process / cerebral cortex GABAergic interneuron development / regulation of respiratory burst / positive regulation of ovarian follicle development / auditory receptor cell morphogenesis / cerebral cortex radially oriented cell migration / erythrocyte enucleation ...embryonic olfactory bulb interneuron precursor migration / anatomical structure arrangement / regulation of ERK5 cascade / angiotensin-activated signaling pathway involved in heart process / cerebral cortex GABAergic interneuron development / regulation of respiratory burst / positive regulation of ovarian follicle development / auditory receptor cell morphogenesis / cerebral cortex radially oriented cell migration / erythrocyte enucleation / regulation of neutrophil migration / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / localization within membrane / kinocilium / regulation of cell adhesion involved in heart morphogenesis / interneuron migration / ruffle assembly / NTRK2 activates RAC1 / NADPH oxidase complex / cochlea morphogenesis / Inactivation of CDC42 and RAC1 / engulfment of apoptotic cell / regulation of hydrogen peroxide metabolic process / regulation of neuron maturation / respiratory burst / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / positive regulation of skeletal muscle acetylcholine-gated channel clustering / ruffle organization / epithelial cell morphogenesis / midbrain dopaminergic neuron differentiation / positive regulation of bicellular tight junction assembly / GTP-dependent protein binding / regulation of Rho protein signal transduction / cell projection assembly / thioesterase binding / regulation of lamellipodium assembly / negative regulation of fibroblast migration / regulation of neuron migration / regulation of stress fiber assembly / RHO GTPases activate CIT / cell-cell junction organization / motor neuron axon guidance / Nef and signal transduction / PCP/CE pathway / Activation of RAC1 / hepatocyte growth factor receptor signaling pathway / sphingosine-1-phosphate receptor signaling pathway / RHO GTPases activate KTN1 / regulation of nitric oxide biosynthetic process / quinolinate biosynthetic process / DCC mediated attractive signaling / MET activates RAP1 and RAC1 / Azathioprine ADME / Sema4D mediated inhibition of cell attachment and migration / hyperosmotic response / CD28 dependent Vav1 pathway / Ephrin signaling / positive regulation of neutrophil chemotaxis / Wnt signaling pathway, planar cell polarity pathway / superoxide anion generation / regulation of receptor signaling pathway via JAK-STAT / lamellipodium assembly / NRAGE signals death through JNK / positive regulation of ruffle assembly / dendrite morphogenesis / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / Activation of RAC1 downstream of NMDARs / positive regulation of Rho protein signal transduction / positive regulation of dendritic spine development / synaptic transmission, GABAergic / pericentriolar material / positive regulation of actin filament polymerization / establishment or maintenance of cell polarity / semaphorin-plexin signaling pathway / RHO GTPases activate PAKs / Rac protein signal transduction / CDC42 GTPase cycle / Sema3A PAK dependent Axon repulsion / ficolin-1-rich granule membrane / EPH-ephrin mediated repulsion of cells / regulation of postsynapse assembly / positive regulation of focal adhesion assembly / RHO GTPases Activate NADPH Oxidases / anatomical structure morphogenesis / regulation of synaptic vesicle endocytosis / regulation of neuronal synaptic plasticity / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / RHO GTPases activate PKNs / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / GPVI-mediated activation cascade / phagocytic cup / positive regulation of lamellipodium assembly / positive regulation of stress fiber assembly / cell projection / actin filament polymerization
Similarity search - Function
Dedicator of cytokinesis C, C2 domain / Dedicator of cytokinesis C/D, N-terminal / Dedicator of cytokinesis C/D, N terminal / 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 ...Dedicator of cytokinesis C, C2 domain / Dedicator of cytokinesis C/D, N-terminal / Dedicator of cytokinesis C/D, N terminal / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.85 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: 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 RW / Shirouzu M
History
DepositionJun 27, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65179.png

Downloads & links

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Map

FileDownload / File: emd_65179.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 340 pix.
= 452.2 Å		1.33 Å/pix.
x 340 pix.
= 452.2 Å		1.33 Å/pix.
x 340 pix.
= 452.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.33 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.0576953 - 0.0948634
Average (Standard dev.)0.000023845949 (±0.0030509369)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 452.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half2 map

Fileemd_65179_half_map_1.map
Annotationhalf2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half1 map

Fileemd_65179_half_map_2.map
Annotationhalf1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DOCK6 tetramer complexed with Rac1

EntireName: DOCK6 tetramer complexed with Rac1
Components
  • Complex: DOCK6 tetramer complexed with Rac1
    • Protein or peptide: Dedicator of cytokinesis protein 6
    • Protein or peptide: Ras-related C3 botulinum toxin substrate 1

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Supramolecule #1: DOCK6 tetramer complexed with Rac1

SupramoleculeName: DOCK6 tetramer complexed with Rac1 / 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: 4 / 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: Ras-related C3 botulinum toxin substrate 1

MacromoleculeName: Ras-related C3 botulinum toxin substrate 1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: small monomeric GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.244258 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSSGSSGMQA IKCVVVGDGA VAKTCLLISY TTNAFPGEYI PTVFDNYSAN VMVDGKPVNL GLWDTAGQED YDRLRPLSYP QTDVFLICF SLVSPASFEN VRAKWYPEVR HHCPNTPIIL VGTKLDLRDD KDTIEKLKEK KLTPITYPQG LAMAKEIGAV K YLECSALT QRGLKTVFDE AIRAVL

UniProtKB: Ras-related C3 botulinum toxin substrate 1

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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
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: 5048 / Average electron dose: 49.5 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: 21977481
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 112745
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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