[English] 日本語
Yorodumi
- EMDB-65174: Structure of DOCK6-Cdc42 complex protomer -

+
Open data


ID or keywords:

Loading...

-
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 / 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)
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: 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

-
Structure visualization

Supplemental images

emd_65174.png

Downloads & links

-
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
Others
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)

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: 0.015
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 °

-
Supplemental data

-
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)

-
Half map: half2 map

Fileemd_65174_half_map_2.map
Annotationhalf2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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)

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more