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Yorodumi- PDB-8zji: Structure of DOCK5/ELMO1/Rac1 core (RhoG/DOCK5/ELMO1/Rac1 dataset... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8zji | ||||||||||||
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Title | Structure of DOCK5/ELMO1/Rac1 core (RhoG/DOCK5/ELMO1/Rac1 dataset, class 1) | ||||||||||||
Components |
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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 / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / podosome assembly / Activated NTRK2 signals through CDK5 / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly ...negative regulation of vascular associated smooth muscle contraction / regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / podosome assembly / Activated NTRK2 signals through CDK5 / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / engulfment of apoptotic cell / NTRK2 activates RAC1 / Inactivation of CDC42 and RAC1 / NADPH oxidase complex / respiratory burst / WNT5:FZD7-mediated leishmania damping / guanyl-nucleotide exchange factor complex / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / hepatocyte growth factor receptor signaling pathway / bone remodeling / myoblast fusion / ruffle organization / cell projection assembly / regulation of stress fiber assembly / thioesterase binding / negative regulation of fibroblast migration / RHO GTPases activate CIT / Azathioprine ADME / sphingosine-1-phosphate receptor signaling pathway / positive regulation of vascular associated smooth muscle cell migration / Nef and signal transduction / motor neuron axon guidance / RHO GTPases activate KTN1 / regulation of nitric oxide biosynthetic process / PCP/CE pathway / Activation of RAC1 / podosome / regulation of lamellipodium assembly / positive regulation of neutrophil chemotaxis / anchoring junction / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / lamellipodium assembly / positive regulation of cell-substrate adhesion / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / Wnt signaling pathway, planar cell polarity pathway / positive regulation of Rho protein signal transduction / NRAGE signals death through JNK / establishment or maintenance of cell polarity / Activation of RAC1 downstream of NMDARs / regulation of cell size / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / phagocytosis, engulfment / positive regulation of epithelial cell migration / Rac protein signal transduction / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / Sema3A PAK dependent Axon repulsion / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate NADPH Oxidases / anatomical structure morphogenesis / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / positive regulation of lamellipodium assembly / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of substrate adhesion-dependent cell spreading / RHO GTPases activate PKNs / GPVI-mediated activation cascade / positive regulation of stress fiber assembly / positive regulation of microtubule polymerization / RAC1 GTPase cycle / EPHB-mediated forward signaling / regulation of cell migration / actin filament polymerization / positive regulation of endothelial cell migration / GTPase activator activity / substrate adhesion-dependent cell spreading / cell chemotaxis / guanyl-nucleotide exchange factor activity / cell-matrix adhesion / small monomeric GTPase / G protein activity / VEGFR2 mediated vascular permeability / secretory granule membrane / actin filament organization / Signal transduction by L1 / cell projection / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cell motility / regulation of actin cytoskeleton organization / RHO GTPases Activate Formins / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.23 Å | ||||||||||||
Authors | Kukimoto-Niino, M. / Katsura, K. / Ishizuka-Katsura, Y. / Mishima-Tsumagari, C. / Yonemochi, M. / Inoue, M. / Nakagawa, R. / Kaushik, R. / Zhang, K.Y.J. / Shirouzu, M. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: J Biol Chem / Year: 2024 Title: RhoG facilitates a conformational transition in the guanine nucleotide exchange factor complex DOCK5/ELMO1 to an open state. Authors: Mutsuko Kukimoto-Niino / Kazushige Katsura / Yoshiko Ishizuka-Katsura / Chiemi Mishima-Tsumagari / Mayumi Yonemochi / Mio Inoue / Reiko Nakagawa / Rahul Kaushik / Kam Y J Zhang / Mikako Shirouzu / Abstract: The dedicator of cytokinesis (DOCK)/engulfment and cell motility (ELMO) complex serves as a guanine nucleotide exchange factor (GEF) for the GTPase Rac. RhoG, another GTPase, activates the ELMO-DOCK- ...The dedicator of cytokinesis (DOCK)/engulfment and cell motility (ELMO) complex serves as a guanine nucleotide exchange factor (GEF) for the GTPase Rac. RhoG, another GTPase, activates the ELMO-DOCK-Rac pathway during engulfment and migration. Recent cryo-EM structures of the DOCK2/ELMO1 and DOCK2/ELMO1/Rac1 complexes have identified closed and open conformations that are key to understanding the autoinhibition mechanism. Nevertheless, the structural details of RhoG-mediated activation of the DOCK/ELMO complex remain elusive. Herein, we present cryo-EM structures of DOCK5/ELMO1 alone and in complex with RhoG and Rac1. The DOCK5/ELMO1 structure exhibits a closed conformation similar to that of DOCK2/ELMO1, suggesting a shared regulatory mechanism of the autoinhibitory state across DOCK-A/B subfamilies (DOCK1-5). Conversely, the RhoG/DOCK5/ELMO1/Rac1 complex adopts an open conformation that differs from that of the DOCK2/ELMO1/Rac1 complex, with RhoG binding to both ELMO1 and DOCK5. The alignment of the DOCK5 phosphatidylinositol (3,4,5)-trisphosphate binding site with the RhoG C-terminal lipidation site suggests simultaneous binding of RhoG and DOCK5/ELMO1 to the plasma membrane. Structural comparison of the apo and RhoG-bound states revealed that RhoG facilitates a closed-to-open state conformational change of DOCK5/ELMO1. Biochemical and surface plasmon resonance (SPR) assays confirm that RhoG enhances the Rac GEF activity of DOCK5/ELMO1 and increases its binding affinity for Rac1. Further analysis of structural variability underscored the conformational flexibility of the DOCK5/ELMO1/Rac1 complex core, potentially facilitating the proximity of the DOCK5 GEF domain to the plasma membrane. These findings elucidate the structural mechanism underlying the RhoG-induced allosteric activation and membrane binding of the DOCK/ELMO complex. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
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PDBx/mmCIF format | 8zji.cif.gz | 742.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8zji.ent.gz | 594.1 KB | Display | PDB format |
PDBx/mmJSON format | 8zji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8zji_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8zji_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8zji_validation.xml.gz | 134.2 KB | Display | |
Data in CIF | 8zji_validation.cif.gz | 202 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/8zji ftp://data.pdbj.org/pub/pdb/validation_reports/zj/8zji | HTTPS FTP |
-Related structure data
Related structure data | 60146MC 8jhkC 8xm7C 8zj2C 8zjjC 8zjkC 8zjlC 8zjmC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 #2: Protein | 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 #3: Protein | 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 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: DOCK5/ELMO1/Rac1 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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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 | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 11976 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2483502 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 133323 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7DPA Accession code: 7DPA / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||
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