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- EMDB-63477: DOCK5/ELMO1 complex with RhoG and Rac1 on lipid membrane -

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Basic information

Entry
Database: EMDB / ID: EMD-63477
TitleDOCK5/ELMO1 complex with RhoG and Rac1 on lipid membrane
Map data
Sample
  • Complex: DOCK5/ELMO1 complex with RhoG and Rac1 on lipid membrane
    • Protein or peptide: Engulfment and cell motility protein 1
    • Protein or peptide: Dedicator of cytokinesis protein 5
    • Protein or peptide: Rho-related GTP-binding protein RhoG
KeywordsComplex / Rho-GTPase / GEF / Lipid membrane / SIGNALING PROTEIN
Function / homology
Function and homology information


regulation of ruffle assembly / negative regulation of vascular associated smooth muscle contraction / podosome assembly / cortical cytoskeleton organization / guanyl-nucleotide exchange factor complex / activation of GTPase activity / bone remodeling / myoblast fusion / Nef and signal transduction / positive regulation of vascular associated smooth muscle cell migration ...regulation of ruffle assembly / negative regulation of vascular associated smooth muscle contraction / podosome assembly / cortical cytoskeleton organization / guanyl-nucleotide exchange factor complex / activation of GTPase activity / bone remodeling / myoblast fusion / Nef and signal transduction / positive regulation of vascular associated smooth muscle cell migration / RHO GTPases activate KTN1 / podosome / anchoring junction / phagocytosis, engulfment / establishment or maintenance of cell polarity / Rac protein signal transduction / positive regulation of epithelial cell migration / regulation of postsynapse assembly / RHOG GTPase cycle / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / GPVI-mediated activation cascade / Rho protein signal transduction / RAC1 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / GTPase activator activity / secretory granule membrane / actin filament organization / guanyl-nucleotide exchange factor activity / cell chemotaxis / regulation of actin cytoskeleton organization / positive regulation of protein localization to plasma membrane / cell projection / FCGR3A-mediated phagocytosis / cell motility / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / small GTPase binding / VEGFA-VEGFR2 Pathway / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / PIP3 activates AKT signaling / regulation of cell shape / Factors involved in megakaryocyte development and platelet production / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / actin cytoskeleton organization / cytoplasmic vesicle / cytoskeleton / postsynapse / focal adhesion / GTPase activity / positive regulation of cell population proliferation / apoptotic process / Neutrophil degranulation / protein kinase binding / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / GTP binding / glutamatergic synapse / extracellular exosome / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Rho-related GTP-binding protein RhoG / Dedicator of cytokinesis protein 5 / : / Dedicator of cytokinesis, N-terminal domain / Dedicator of cytokinesis, N-terminal, subdomain 1 / : / DOCK N-terminus / Dedicator of cytokinesis (DOCK) TPR region / ELMO domain / ELMO, armadillo-like helical domain ...Rho-related GTP-binding protein RhoG / Dedicator of cytokinesis protein 5 / : / Dedicator of cytokinesis, N-terminal domain / Dedicator of cytokinesis, N-terminal, subdomain 1 / : / DOCK N-terminus / Dedicator of cytokinesis (DOCK) TPR region / ELMO domain / ELMO, armadillo-like helical domain / : / ELMO/CED-12 family / ELMO, armadillo-like helical domain / ELMO domain profile. / 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. / Pleckstrin homology domain / Small GTPase Rho / Small GTPase Rho domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / C2 domain superfamily / Pleckstrin homology domain / SH3 domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Armadillo-like helical / Small GTP-binding protein domain / PH-like domain superfamily / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Rho-related GTP-binding protein RhoG / Engulfment and cell motility protein 1 / Dedicator of cytokinesis protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.52 Å
AuthorsShinoda T / Katsura K / Kukimoto-Niino M / Shirouzu M
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Science and TechnologyCREST JPMJCR22E3 Japan
CitationJournal: To Be Published
Title: Conformational alteration of DOCK5-ELMO1 signalosome on lipid membrane
Authors: Shinoda T / Katsura K / Ishizuka-Katsura Y / Hanada K / Yonemochi M / Miyamoto Y / Kukimoto-Niino M / Yamauchi J / Shirouzu M
History
DepositionFeb 18, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63477.png

Downloads & links

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Map

FileDownload / File: emd_63477.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 478.8 Å		1.33 Å/pix.
x 360 pix.
= 478.8 Å		1.33 Å/pix.
x 360 pix.
= 478.8 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: 0.4
Minimum - Maximum-3.5676033 - 5.1812515
Average (Standard dev.)-0.00025185134 (±0.06383253)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 478.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63477_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63477_half_map_2.map
Projections & Slices
AxesZYX

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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 : DOCK5/ELMO1 complex with RhoG and Rac1 on lipid membrane

EntireName: DOCK5/ELMO1 complex with RhoG and Rac1 on lipid membrane
Components
  • Complex: DOCK5/ELMO1 complex with RhoG and Rac1 on lipid membrane
    • Protein or peptide: Engulfment and cell motility protein 1
    • Protein or peptide: Dedicator of cytokinesis protein 5
    • Protein or peptide: Rho-related GTP-binding protein RhoG

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Supramolecule #1: DOCK5/ELMO1 complex with RhoG and Rac1 on lipid membrane

SupramoleculeName: DOCK5/ELMO1 complex with RhoG and Rac1 on lipid membrane
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Engulfment and cell motility protein 1

MacromoleculeName: Engulfment and cell motility protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.379797 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GGSVGSMPPP ADIVKVAIEW PGAYPKLMEI DQKKPLSAII KEVCDGWSLA NHEYFALQHA DSSNFYITEK NRNEIKNGTI LRLTTSPAQ NAQQLHERIQ SSSMDAKLEA LKDLASLSRD VTFAQEFINL DGISLLTQMV ESGTERYQKL QKIMKPCFGD M LSFTLTAF ...String:
GGSVGSMPPP ADIVKVAIEW PGAYPKLMEI DQKKPLSAII KEVCDGWSLA NHEYFALQHA DSSNFYITEK NRNEIKNGTI LRLTTSPAQ NAQQLHERIQ SSSMDAKLEA LKDLASLSRD VTFAQEFINL DGISLLTQMV ESGTERYQKL QKIMKPCFGD M LSFTLTAF VELMDHGIVS WDTFSVAFIK KIASFVNKSA IDISILQRSL AILESMVLNS HDLYQKVAQE ITIGQLIPHL QG SDQEIQT YTIAVINALF LKAPDERRQE MANILAQKQL RSIILTHVIR AQRAINNEMA HQLYVLQVLT FNLLEDRMMT KMD PQDQAQ RDIIFELRRI AFDAESEPNN SSGSMEKRKS MYTRDYKKLG FINHVNPAMD FTQTPPGMLA LDNMLYFAKH HQDA YIRIV LENSSREDKH ECPFGRSSIE LTKMLCEILK VGELPSETCN DFHPMFFTHD RSFEEFFCIC IQLLNKTWKE MRATS EDFN KVMQVVKEQV MRALTTKPSS LDQFKSKLQN LSYTEILKIR QSERMNQEDF QSRPILELKE KIQPEILELI KQQRLN RLV EGTCFRKLNA RRRQDKFWYC RLSPNHKVLH YGDLEESPQG EVPHDSLQDK LPVADIKAVV TGKDCPHMKE KGALKQN KE VLELAFSILY DSNCQLNFIA PDKHEYCIWT DGLNALLGKD MMSDLTRNDL DTLLSMEIKL RLLDLENIQI PDAPPPIP K EPSNYDFVYD CN

UniProtKB: Engulfment and cell motility protein 1

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Macromolecule #2: Dedicator of cytokinesis protein 5

MacromoleculeName: Dedicator of cytokinesis protein 5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 216.022406 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GGSGGSMARW IPTKRQKYGV AIYNYNASQD VELSLQIGDT VHILEMYEGW YRGYTLQNKS KKGIFPETYI HLKEATVEDL GQHETVIPG ELPLVQELTS TLREWAVIWR KLYVNNKLTL FRQLQQMTYS LIEWRSQILS GTLPKDELAE LKKKVTAKID H GNRMLGLD ...String:
GGSGGSMARW IPTKRQKYGV AIYNYNASQD VELSLQIGDT VHILEMYEGW YRGYTLQNKS KKGIFPETYI HLKEATVEDL GQHETVIPG ELPLVQELTS TLREWAVIWR KLYVNNKLTL FRQLQQMTYS LIEWRSQILS GTLPKDELAE LKKKVTAKID H GNRMLGLD LVVRDDNGNI LDPDETSTIA LFKAHEVASK RIEEKIQEEK SILQNLDLRG QSIFSTIHTY GLYVNFKNFV CN IGEDAEL FMALYDPDQS TFISENYLIR WGSNGMPKEI EKLNNLQAVF TDLSSMDLIR PRVSLVCQIV RVGHMELKEG KKH TCGLRR PFGVAVMDIT DIIHGKVDDE EKQHFIPFQQ IAMETYIRQR QLIMSPLITS HVIGENEPLT SVLNKVIAAK EVNH KGQGL WVSLKLLPGD LTQVQKNFSH LVDRSTAIAR KMGFPEIILP GDVRNDIYVT LIHGEFDKGK KKTPKNVEVT MSVHD EEGK LLEKAIHPGA GYEGISEYKS VVYYQVKQPC WYETVKVSIA IEEVTRCHIR FTFRHRSSQE TRDKSERAFG VAFVKL MNP DGTTLQDGRH DLVVYKGDNK KMEDAKFYLT LPGTKMEMEE KELQASKNLV TFTPSKDSTK DSFQIATLIC STKLTQN VD LLGLLNWRSN SQNIKHNLKK LMEVDGGEIV KFLQDTLDAL FNIMMEMSDS ETYDFLVFDA LVFIISLIGD IKFQHFNP V LETYIYKHFS ATLAYVKLSK VLNFYVANAD DSSKTELLFA ALKALKYLFR FIIQSRVLYL RFYGQSKDGD EFNNSIRQL FLAFNMLMDR PLEEAVKIKG AALKYLPSII NDVKLVFDPV ELSVLFCKFI QSIPDNQLVR QKLNCMTKIV ESTLFRQSEC REVLLPLLT DQLSGQLDDN SNKPDHEASS QLLSNILEVL DRKDVGATAV HIQLIMERLL RRINRTVIGM NRQSPHIGSF V ACMIALLQ QMDDSHYSHY ISTFKTRQDI IDFLMETFIM FKDLIGKNVY AKDWMVMNMT QNRVFLRAIN QFAEVLTRFF MD QASFELQ LWNNYFHLAV AFLTHESLQL ETFSQAKRNK IVKKYGDMRK EIGFRIRDMW YNLGPHKIKF IPSMVGPILE VTL TPEVEL RKATIPIFFD MMQCEFNFSG NGNFHMFENE LITKLDQEVE GGRGDEQYKV LLEKLLLEHC RKHKYLSSSG EVFA LLVSS LLENLLDYRT IIMQDESKEN RMSCTVNVLN FYKEKKREDI YIRYLYKLRD LHRDCENYTE AAYTLLLHAE LLQWS DKPC VPHLLQRDSY YVYTQQELKE KLYQEIISYF DKGKMWEKAI KLSKELAETY ESKVFDYEGL GNLLKKRASF YENIIK AMR PQPEYFAVGY YGQGFPSFLR NKIFIYRGKE YERREDFSLR LLTQFPNAEK MTSTTPPGED IKSSPKQYMQ CFTVKPV MS LPPSYKDKPV PEQILNYYRA NEVQQFRYSR PFRKGEKDPD NEFATMWIER TTYTTAYTFP GILKWFEVKQ ISTEEISP L ENAIETMELT NERISNCVQQ HAWDRSLSVH PLSMLLSGIV DPAVMGGFSN YEKAFFTEKY LQEHPEDQEK VELLKRLIA LQMPLLTEGI RIHGEKLTEQ LKPLHERLSS CFRELKEKVE KHYGVITLPP NLTERKQSRT GSIVLPYIMS STLRRLSITS VTSSVVSTS SNSSDNAPSR PGSDGSILEP LLERRASSGA RVEDLSLREE NSENRISKFK RKDWSLSKSQ VIAEKAPEPD L MSPTRKAQ RPKSLQLMDN RLSPFHGSSP PQSTPLSPPP LTPKATRTLS SPSLQTDGIA ATPVPPPPPP KSKPYEGSQR NS TELAPPL PVRREAKAPP PPPPKARKSG IPTSEPGSQ

UniProtKB: Dedicator of cytokinesis protein 5

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Macromolecule #3: Rho-related GTP-binding protein RhoG

MacromoleculeName: Rho-related GTP-binding protein RhoG / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.692918 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSSGSSGMQS IKCVVVGDGA VGKTCLLICY TTNAFPKEYI PTVFDNYSAQ SAVDGRTVNL NLWDTAGLEE YDRLRTLSYP QTNVFVICF SIASPPSYEN VRHKWHPEVC HHCPDVPILL VGTKKDLRAQ PDTLRRLKEQ GQAPITPQQG QALAKQIHAV R YLECSALQ ...String:
GSSGSSGMQS IKCVVVGDGA VGKTCLLICY TTNAFPKEYI PTVFDNYSAQ SAVDGRTVNL NLWDTAGLEE YDRLRTLSYP QTNVFVICF SIASPPSYEN VRHKWHPEVC HHCPDVPILL VGTKKDLRAQ PDTLRRLKEQ GQAPITPQQG QALAKQIHAV R YLECSALQ QDGVKEVFAE AVRAVLNPTP IKRGRSCILL SGPSSGHHHH HHHHHH

UniProtKB: Rho-related GTP-binding protein RhoG

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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: 7
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 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7dpa

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 55365
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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