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Open data
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Basic information
Entry | Database: PDB / ID: 7dpa | ||||||
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Title | Cryo-EM structure of the human ELMO1-DOCK5-Rac1 complex | ||||||
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![]() | SIGNALING PROTEIN / ELMO / DOCK / GEF / GTPASE / RHO / RAC | ||||||
Function / homology | ![]() negative regulation of vascular associated smooth muscle contraction / embryonic olfactory bulb interneuron precursor migration / anatomical structure arrangement / regulation of ERK5 cascade / angiotensin-activated signaling pathway involved in heart process / positive regulation of ovarian follicle development / cerebral cortex GABAergic interneuron development / regulation of respiratory burst / auditory receptor cell morphogenesis / cerebral cortex radially oriented cell migration ...negative regulation of vascular associated smooth muscle contraction / embryonic olfactory bulb interneuron precursor migration / anatomical structure arrangement / regulation of ERK5 cascade / angiotensin-activated signaling pathway involved in heart process / positive regulation of ovarian follicle development / cerebral cortex GABAergic interneuron development / regulation of respiratory burst / auditory receptor cell morphogenesis / cerebral cortex radially oriented cell migration / erythrocyte enucleation / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / podosome assembly / interneuron migration / regulation of hydrogen peroxide metabolic process / kinocilium / regulation of cell adhesion involved in heart morphogenesis / negative regulation of receptor-mediated endocytosis / engulfment of apoptotic cell / ruffle assembly / NTRK2 activates RAC1 / NADPH oxidase complex / cochlea morphogenesis / Inactivation of CDC42 and RAC1 / regulation of neuron maturation / respiratory burst / guanyl-nucleotide exchange factor complex / WNT5:FZD7-mediated leishmania damping / cortical cytoskeleton organization / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / positive regulation of skeletal muscle acetylcholine-gated channel clustering / hepatocyte growth factor receptor signaling pathway / GTP-dependent protein binding / bone remodeling / midbrain dopaminergic neuron differentiation / ruffle organization / epithelial cell morphogenesis / cell projection assembly / positive regulation of bicellular tight junction assembly / myoblast fusion / thioesterase binding / regulation of lamellipodium assembly / positive regulation of vascular associated smooth muscle cell migration / regulation of stress fiber assembly / regulation of neuron migration / negative regulation of fibroblast migration / RHO GTPases activate CIT / motor neuron axon guidance / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / regulation of nitric oxide biosynthetic process / PCP/CE pathway / Activation of RAC1 / RHO GTPases activate KTN1 / positive regulation of neutrophil chemotaxis / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / cell-cell junction organization / Azathioprine ADME / hyperosmotic response / Sema4D mediated inhibition of cell attachment and migration / positive regulation of cell-substrate adhesion / Ephrin signaling / CD28 dependent Vav1 pathway / positive regulation of ruffle assembly / superoxide anion generation / Wnt signaling pathway, planar cell polarity pathway / podosome / anchoring junction / lamellipodium assembly / regulation of receptor signaling pathway via JAK-STAT / phagocytosis, engulfment / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / NRAGE signals death through JNK / regulation of cell size / dendrite morphogenesis / positive regulation of Rho protein signal transduction / Rho GDP-dissociation inhibitor binding / establishment or maintenance of cell polarity / synaptic transmission, GABAergic / Rac protein signal transduction / positive regulation of actin filament polymerization / positive regulation of dendritic spine development / RHO GTPases activate PAKs / pericentriolar material / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / RHOG GTPase cycle / Sema3A PAK dependent Axon repulsion / positive regulation of epithelial cell migration / RHO GTPases Activate NADPH Oxidases / EPH-ephrin mediated repulsion of cells / regulation of postsynapse assembly / regulation of synaptic vesicle endocytosis / anatomical structure morphogenesis / regulation of neuronal synaptic plasticity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
![]() | 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. | ||||||
![]() | ![]() 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. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 735 KB | Display | ![]() |
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PDB format | ![]() | 585.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 134.5 KB | Display | |
Data in CIF | ![]() | 200.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 30802MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 191492.125 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 20244.258 Da / Num. of mol.: 2 / Mutation: G15A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 84337.719 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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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 |
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Sample preparation
Component | Name: ELMO1-DOCK5-Rac1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
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 % |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / 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) |
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Processing
EM software |
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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 |