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- PDB-9lx0: DOCK5/ELMO1 complex with RhoG and Rac1 on lipid membrane -

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Basic information

Entry
Database: PDB / ID: 9lx0
TitleDOCK5/ELMO1 complex with RhoG and Rac1 on lipid membrane
Components
  • Dedicator of cytokinesis protein 5
  • Engulfment and cell motility protein 1
  • Ras-related C3 botulinum toxin substrate 1
  • Rho-related GTP-binding protein RhoG
KeywordsSIGNALING PROTEIN / Complex / Rho-GTPase / GEF / Lipid membrane
Function / homology
Function and homology information


guanyl nucleotide exchange factor activator activity / regulation of vasculogenesis / negative regulation of vascular associated smooth muscle contraction / regulation of respiratory burst / positive regulation of ovarian follicle development / regulation of neutrophil migration / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / ruffle assembly / localization within membrane ...guanyl nucleotide exchange factor activator activity / regulation of vasculogenesis / negative regulation of vascular associated smooth muscle contraction / regulation of respiratory burst / positive regulation of ovarian follicle development / regulation of neutrophil migration / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / ruffle assembly / localization within membrane / kinocilium / regulation of cell adhesion involved in heart morphogenesis / NTRK2 activates RAC1 / NADPH oxidase complex / Inactivation of CDC42 and RAC1 / regulation of hydrogen peroxide metabolic process / engulfment of apoptotic cell / guanyl-nucleotide exchange factor complex / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / cell projection assembly / respiratory burst / activation of GTPase activity / motor neuron axon guidance / ruffle organization / myoblast fusion / midbrain dopaminergic neuron differentiation / positive regulation of bicellular tight junction assembly / GTP-dependent protein binding / negative regulation of fibroblast migration / thioesterase binding / regulation of stress fiber assembly / regulation of lamellipodium assembly / RHO GTPases activate CIT / Nef and signal transduction / Activation of RAC1 / PCP/CE pathway / hepatocyte growth factor receptor signaling pathway / sphingosine-1-phosphate receptor signaling pathway / podosome / RHO GTPases activate KTN1 / superoxide anion generation / DCC mediated attractive signaling / MET activates RAP1 and RAC1 / positive regulation of vascular associated smooth muscle cell migration / regulation of nitric oxide biosynthetic process / Azathioprine ADME / Sema4D mediated inhibition of cell attachment and migration / forebrain development / CD28 dependent Vav1 pathway / Ephrin signaling / positive regulation of neutrophil chemotaxis / positive regulation of ruffle assembly / Wnt signaling pathway, planar cell polarity pathway / lamellipodium assembly / phagocytosis, engulfment / regulation of receptor signaling pathway via JAK-STAT / NRAGE signals death through JNK / Rho GDP-dissociation inhibitor binding / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / positive regulation of Rho protein signal transduction / pericentriolar material / establishment or maintenance of cell polarity / Rac protein signal transduction / positive regulation of epithelial cell migration / RHO GTPases activate PAKs / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / ficolin-1-rich granule membrane / regulation of postsynapse assembly / positive regulation of focal adhesion assembly / RHO GTPases Activate NADPH Oxidases / regulation of synaptic vesicle endocytosis / anatomical structure morphogenesis / RHO GTPases Activate WASPs and WAVEs / positive regulation of lamellipodium assembly / RHO GTPases activate IQGAPs / Rho protein signal transduction / positive regulation of stress fiber assembly / RHO GTPases activate PKNs / GPVI-mediated activation cascade / substrate adhesion-dependent cell spreading / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / phagocytic cup / cell projection / positive regulation of substrate adhesion-dependent cell spreading / actin filament polymerization / RAC1 GTPase cycle / cell-matrix adhesion / EPHB-mediated forward signaling / regulation of cell migration / positive regulation of endothelial cell migration / guanyl-nucleotide exchange factor activity / secretory granule membrane / actin filament organization / positive regulation of insulin secretion involved in cellular response to glucose stimulus
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 protein N-terminal Ras-binding domain / ELMO 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 protein N-terminal Ras-binding domain / ELMO domain / ELMO, armadillo-like helical domain / : / ELMO/CED-12 family / ELMO, armadillo-like helical domain / ELMO domain profile. / Pleckstrin homology domain / 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. / 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
Ras-related C3 botulinum toxin substrate 1 / 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: 6.98 Å
AuthorsShinoda, T. / Katsura, K. / Kukimoto-Niino, M. / Shirouzu, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyCREST JPMJCR22E3 Japan
CitationJournal: Commun Biol / Year: 2025
Title: Conformational alteration of DOCK5•ELMO1 signalosome on lipid membrane.
Authors: Takehiro Shinoda / Kazushige Katsura / Yoshiko Ishizuka-Katsura / Kazuharu Hanada / Mayumi Yonemochi / Yuki Miyamoto / Mutsuko Kukimoto-Niino / Junji Yamauchi / Mikako Shirouzu /
Abstract: The DOCK protein family activates Rho small GTPases through guanine nucleotide exchange factor (GEF) activity. DOCK is thought to exert its GEF activity at the plasma membrane. However, the mechanism ...The DOCK protein family activates Rho small GTPases through guanine nucleotide exchange factor (GEF) activity. DOCK is thought to exert its GEF activity at the plasma membrane. However, the mechanism by which DOCK activity on the plasma membrane is regulated remains unclear. Herein, we present a new conformation in which DOCK5, ELMO1, RhoG, and Rac1 are aligned on a plane and symmetrically flattened, as revealed by cryo-EM using a lipid membrane-coated grid. The major conformational change leading to this structure results from rotation of each DOCK5•ELMO1 hinge site through interactions with the membrane. Biochemical and cellular experiments indicate that conformational changes driven by acidic lipids are important for regulating the GEF activity of the DOCK5•ELMO1 complex on the plasma membrane and are essential for its downstream signalling. This approach also enables the analysis of large lipid-associated complexes, such as signalosomes, and will aid studies of membrane-dependent signalling assemblies.
History
DepositionFeb 17, 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
Revision 1.1Nov 26, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
D: Ras-related C3 botulinum toxin substrate 1
E: Engulfment and cell motility protein 1
F: Dedicator of cytokinesis protein 5
G: Rho-related GTP-binding protein RhoG
H: Ras-related C3 botulinum toxin substrate 1


Theoretical massNumber of molelcules
Total (without water)694,2658
Polymers694,2658
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.: 2
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.: 2
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.: 2 / 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
#4: Protein Ras-related C3 botulinum toxin substrate 1 / Cell migration-inducing gene 5 protein / Ras-like protein TC25 / p21-Rac1


Mass: 23037.535 Da / Num. of mol.: 2 / Mutation: G15A, C189S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1, TC25, MIG5 / Production host: Escherichia coli (E. coli) / References: UniProt: P63000, small monomeric GTPase
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
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
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: 6.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55365 / Symmetry type: POINT
RefinementHighest resolution: 6.98 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_d0.00245006
ELECTRON MICROSCOPYf_angle_d0.44960826
ELECTRON MICROSCOPYf_dihedral_angle_d11.32217078
ELECTRON MICROSCOPYf_chiral_restr0.0386786
ELECTRON MICROSCOPYf_plane_restr0.0037800

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