|Entry||Database: PDB / ID: 7dpa|
|Title||Cryo-EM structure of the human ELMO1-DOCK5-Rac1 complex|
|Keywords||SIGNALING PROTEIN / ELMO / DOCK / GEF / GTPASE / RHO / RAC|
|Function / homology|
Function and homology information
negative regulation of vascular associated smooth muscle contraction / regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / engulfment of apoptotic cell / regulation of hydrogen peroxide metabolic process ...negative regulation of vascular associated smooth muscle contraction / regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / engulfment of apoptotic cell / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / Rho GDP-dissociation inhibitor binding / positive regulation of vascular associated smooth muscle cell migration / Inactivation of CDC42 and RAC1 / WNT5:FZD7-mediated leishmania damping / guanyl-nucleotide exchange factor complex / respiratory burst / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / PCP/CE pathway / cell projection assembly / RHO GTPases activate CIT / RHO GTPases activate KTN1 / cortical cytoskeleton organization / ruffle organization / hepatocyte growth factor receptor signaling pathway / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / Azathioprine ADME / regulation of stress fiber assembly / negative regulation of fibroblast migration / sphingosine-1-phosphate receptor signaling pathway / thioesterase binding / Wnt signaling pathway, planar cell polarity pathway / regulation of lamellipodium assembly / Nef and signal transduction / motor neuron axon guidance / Sema4D mediated inhibition of cell attachment and migration / Activation of RAC1 / positive regulation of Rho protein signal transduction / positive regulation of cell-substrate adhesion / Ephrin signaling / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / CD28 dependent Vav1 pathway / lamellipodium assembly / Activation of RAC1 downstream of NMDARs / semaphorin-plexin signaling pathway / NRAGE signals death through JNK / regulation of cell size / Rac protein signal transduction / DSCAM interactions / positive regulation of lamellipodium assembly / establishment or maintenance of cell polarity / positive regulation of epithelial cell migration / small GTPase mediated signal transduction / RHO GTPases activate PAKs / ficolin-1-rich granule membrane / regulation of catalytic activity / positive regulation of focal adhesion assembly / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / RHO GTPases activate IQGAPs / anatomical structure morphogenesis / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / RHO GTPases Activate WASPs and WAVEs / RHO GTPases Activate NADPH Oxidases / RHO GTPases activate PKNs / localization / regulation of actin cytoskeleton organization / GPVI-mediated activation cascade / EPHB-mediated forward signaling / positive regulation of microtubule polymerization / G protein activity / positive regulation of stress fiber assembly / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / RAC1 GTPase cycle / neuron migration / actin filament polymerization / GTPase activator activity / small monomeric GTPase / guanyl-nucleotide exchange factor activity / cell-matrix adhesion / substrate adhesion-dependent cell spreading / cell motility / actin filament organization / phagocytosis, engulfment / secretory granule membrane / RHO GTPases Activate Formins / VEGFR2 mediated vascular permeability / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of endothelial cell migration / Signal transduction by L1 / cell projection / FCERI mediated MAPK activation / MAPK6/MAPK4 signaling / FCGR3A-mediated phagocytosis / Signaling by SCF-KIT / trans-Golgi network
Similarity search - Function
: / Dedicator of cytokinesis protein 5 / Engulfment and cell motility protein 1 / Dedicator of cytokinesis, N-terminal domain / Dedicator of cytokinesis, N-terminal, subdomain 1 / DOCK N-terminus / ELMO domain / ELMO/CED-12 family / ELMO domain profile. / ELMO, armadillo-like helical domain ...: / Dedicator of cytokinesis protein 5 / Engulfment and cell motility protein 1 / Dedicator of cytokinesis, N-terminal domain / Dedicator of cytokinesis, N-terminal, subdomain 1 / DOCK N-terminus / ELMO domain / ELMO/CED-12 family / ELMO domain profile. / ELMO, armadillo-like helical domain / ELMO, armadillo-like helical domain / Dedicator of cytokinesis / C2 DOCK-type domain / DOCKER domain / Dedicator of cytokinesis, C-terminal, lobe A / Dedicator of cytokinesis, C-terminal, lobe C / DHR-2, Lobe A / C2 domain in Dock180 and Zizimin proteins / C2 DOCK-type domain profile. / DOCKER domain profile. / Pleckstrin homology domain / small GTPase Rho family profile. / Small GTPase Rho / C2 domain superfamily / Rho (Ras homology) subfamily of Ras-like small GTPases / Pleckstrin homology domain / Small GTPase / Ras family / SH3 domain / Src homology 3 domains / Armadillo-like helical / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 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 / Engulfment and cell motility protein 1 / Dedicator of cytokinesis protein 5
Similarity search - Component
|Biological species||Homo sapiens (human)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å|
|Authors||Kukimoto-Niino, M. / Katsura, K. / Kaushik, R. / Ehara, H. / Yokoyama, T. / Uchikubo-Kamo, T. / Mishima-Tsumagari, C. / Yonemochi, M. / Ikeda, M. / Hanada, K. ...Kukimoto-Niino, M. / Katsura, K. / Kaushik, R. / Ehara, H. / Yokoyama, T. / Uchikubo-Kamo, T. / Mishima-Tsumagari, C. / Yonemochi, M. / Ikeda, M. / Hanada, K. / Zhang, K.Y.J. / Shirouzu, M.|
|Citation||Journal: Sci Adv / Year: 2021|
Title: Cryo-EM structure of the human ELMO1-DOCK5-Rac1 complex.
Authors: Mutsuko Kukimoto-Niino / Kazushige Katsura / Rahul Kaushik / Haruhiko Ehara / Takeshi Yokoyama / Tomomi Uchikubo-Kamo / Reiko Nakagawa / Chiemi Mishima-Tsumagari / Mayumi Yonemochi / Mariko ...Authors: Mutsuko Kukimoto-Niino / Kazushige Katsura / Rahul Kaushik / Haruhiko Ehara / Takeshi Yokoyama / Tomomi Uchikubo-Kamo / Reiko Nakagawa / Chiemi Mishima-Tsumagari / Mayumi Yonemochi / Mariko Ikeda / Kazuharu Hanada / Kam Y J Zhang / Mikako Shirouzu /
Abstract: The dedicator of cytokinesis (DOCK) family of guanine nucleotide exchange factors (GEFs) promotes cell motility, phagocytosis, and cancer metastasis through activation of Rho guanosine ...The dedicator of cytokinesis (DOCK) family of guanine nucleotide exchange factors (GEFs) promotes cell motility, phagocytosis, and cancer metastasis through activation of Rho guanosine triphosphatases. Engulfment and cell motility (ELMO) proteins are binding partners of DOCK and regulate Rac activation. Here, we report the cryo-electron microscopy structure of the active ELMO1-DOCK5 complex bound to Rac1 at 3.8-Å resolution. The C-terminal region of ELMO1, including the pleckstrin homology (PH) domain, aids in the binding of the catalytic DOCK homology region 2 (DHR-2) domain of DOCK5 to Rac1 in its nucleotide-free state. A complex α-helical scaffold between ELMO1 and DOCK5 stabilizes the binding of Rac1. Mutagenesis studies revealed that the PH domain of ELMO1 enhances the GEF activity of DOCK5 through specific interactions with Rac1. The structure provides insights into how ELMO modulates the biochemical activity of DOCK and how Rac selectivity is achieved by ELMO.
|Structure viewer||Molecule: |
Downloads & links
A: Dedicator of cytokinesis protein 5
B: Ras-related C3 botulinum toxin substrate 1
C: Engulfment and cell motility protein 1
D: Dedicator of cytokinesis protein 5
E: Ras-related C3 botulinum toxin substrate 1
F: Engulfment and cell motility protein 1
Mass: 191492.125 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
Mass: 20244.258 Da / Num. of mol.: 2 / Mutation: G15A
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
Mass: 84337.719 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
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: ELMO1-DOCK5-Rac1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT|
|Molecular weight||Experimental value: NO|
|Source (natural)||Organism: Homo sapiens (human)|
|Source (recombinant)||Organism: Homo sapiens (human)|
|Buffer solution||pH: 8|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3|
|Vitrification||Cryogen name: ETHANE / Humidity: 100 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 105000 X / Calibrated defocus min: 0.5 nm / Calibrated defocus max: 3 nm|
|Image recording||Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Particle selection||Num. of particles selected: 2145777|
|Symmetry||Point symmetry: C2 (2 fold cyclic)|
|3D reconstruction||Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 149846 / Num. of class averages: 1 / Symmetry type: POINT|
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