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- PDB-9lxh: DOCK5/ELMO1 complex with RhoG and Rac1 on lipid membrane -

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Basic information

Entry
Database: PDB / ID: 9lxh
TitleDOCK5/ELMO1 complex with RhoG and Rac1 on lipid membrane
Components
  • Dedicator of cytokinesis protein 5
  • Engulfment and cell motility protein 1
  • Rho-related GTP-binding protein RhoG
KeywordsSIGNALING PROTEIN / Complex / Rho-GTPase / GEF / Lipid membrane
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.52 Å
AuthorsShinoda, T. / Katsura, K. / Kukimoto-Niino, M. / Shirouzu, M.
Funding support Japan, 1items
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, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Engulfment and cell motility protein 1
B: Dedicator of cytokinesis protein 5
C: Rho-related GTP-binding protein RhoG


Theoretical massNumber of molelcules
Total (without water)324,0953
Polymers324,0953
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Engulfment and cell motility protein 1 / Protein ced-12 homolog


Mass: 84379.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELMO1, KIAA0281 / Production host: Homo sapiens (human) / References: UniProt: Q92556
#2: Protein Dedicator of cytokinesis protein 5


Mass: 216022.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DOCK5 / Production host: Homo sapiens (human) / References: UniProt: Q9H7D0
#3: Protein Rho-related GTP-binding protein RhoG


Mass: 23692.918 Da / Num. of mol.: 1 / Mutation: Q61L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOG, ARHG / Production host: Escherichia coli (E. coli) / References: UniProt: P84095
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: DOCK5/ELMO1 complex with RhoG and Rac1 on lipid membrane
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55365 / Symmetry type: POINT
RefinementHighest resolution: 7.52 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00217783
ELECTRON MICROSCOPYf_angle_d0.49624021
ELECTRON MICROSCOPYf_dihedral_angle_d12.8186741
ELECTRON MICROSCOPYf_chiral_restr0.0392701
ELECTRON MICROSCOPYf_plane_restr0.0043082

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