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- EMDB-65180: Structure of DOCK6 octamer -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-65180
TitleStructure of DOCK6 octamer
Map datapostprocess map
Sample
  • Complex: DOCK6 octamer
    • Protein or peptide: Dedicator of cytokinesis protein 6
KeywordsDOCK / GEF / Rho / small GTPase / Rac / Cdc42 / SIGNALING PROTEIN
Function / homology
Function and homology information


regulation of Rho protein signal transduction / small GTPase-mediated signal transduction / CDC42 GTPase cycle / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity / Factors involved in megakaryocyte development and platelet production / perinuclear region of cytoplasm / cytosol
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. / C2 domain superfamily
Similarity search - Domain/homology
Dedicator of cytokinesis protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.53 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_65180.png

Downloads & links

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Map

FileDownload / File: emd_65180.map.gz / Format: CCP4 / Size: 149.9 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 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: 0.008
Minimum - Maximum-0.037920155 - 0.07472
Average (Standard dev.)0.00006637662 (±0.0026976424)
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_65180_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_65180_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 octamer

EntireName: DOCK6 octamer
Components
  • Complex: DOCK6 octamer
    • Protein or peptide: Dedicator of cytokinesis protein 6

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Supramolecule #1: DOCK6 octamer

SupramoleculeName: DOCK6 octamer / 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: 8 / 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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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: 4317 / Average electron dose: 50.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 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: 1793089
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: 7.53 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 102384
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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