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- PDB-7use: Cryo-EM structure of WAVE regulatory complex with Rac1 bound on b... -
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Basic information
Entry | Database: PDB / ID: 7use | ||||||
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Title | Cryo-EM structure of WAVE regulatory complex with Rac1 bound on both A and D site | ||||||
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![]() | CELL INVASION / actin regulator / GTPase binding protein / cytoskeletal regulator | ||||||
Function / homology | ![]() peripheral region of growth cone / negative regulation of synaptic vesicle recycling / SCAR complex / positive regulation of neurotrophin TRK receptor signaling pathway / lamellipodium morphogenesis / positive regulation of Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / modification of synaptic structure / regulation of actin polymerization or depolymerization / central region of growth cone ...peripheral region of growth cone / negative regulation of synaptic vesicle recycling / SCAR complex / positive regulation of neurotrophin TRK receptor signaling pathway / lamellipodium morphogenesis / positive regulation of Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / modification of synaptic structure / regulation of actin polymerization or depolymerization / central region of growth cone / modification of postsynaptic actin cytoskeleton / regulation of respiratory burst / dendrite extension / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / regulation of translation at postsynapse, modulating synaptic transmission / Activated NTRK2 signals through CDK5 / filopodium tip / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / Inactivation of CDC42 and RAC1 / NADPH oxidase complex / engulfment of apoptotic cell / WNT5:FZD7-mediated leishmania damping / respiratory burst / regulation of modification of postsynaptic actin cytoskeleton / regulation of actin filament polymerization / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / hepatocyte growth factor receptor signaling pathway / RNA 7-methylguanosine cap binding / ruffle organization / thioesterase binding / regulation of stress fiber assembly / negative regulation of fibroblast migration / cell projection assembly / RHO GTPases activate CIT / axon extension / sphingosine-1-phosphate receptor signaling pathway / Nef and signal transduction / PCP/CE pathway / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / RHO GTPases activate KTN1 / Activation of RAC1 / motor neuron axon guidance / positive regulation of ruffle assembly / regulation of lamellipodium assembly / positive regulation of dendrite development / Azathioprine ADME / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / regulation of myelination / protein kinase A binding / lamellipodium assembly / cortical actin cytoskeleton organization / regulation of cell size / establishment or maintenance of cell polarity / DSCAM interactions / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / positive regulation of Rho protein signal transduction / positive regulation of actin filament polymerization / NRAGE signals death through JNK / Rac protein signal transduction / protein kinase A regulatory subunit binding / dendritic growth cone / filamentous actin / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / lamellipodium membrane / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / ficolin-1-rich granule membrane / excitatory synapse / RHOG GTPase cycle / RHO GTPases Activate NADPH Oxidases / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / localization / RAC3 GTPase cycle / RHO GTPases activate IQGAPs / anatomical structure morphogenesis / positive regulation of axon extension / axonal growth cone / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / signaling adaptor activity / response to electrical stimulus / positive regulation of substrate adhesion-dependent cell spreading Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
![]() | Ding, B. / Yang, S. / Chen, B. / Chowdhury, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structures reveal a key mechanism of WAVE regulatory complex activation by Rac1 GTPase. Authors: Bojian Ding / Sheng Yang / Matthias Schaks / Yijun Liu / Abbigale J Brown / Klemens Rottner / Saikat Chowdhury / Baoyu Chen / ![]() ![]() ![]() Abstract: The Rho-family GTPase Rac1 activates the WAVE regulatory complex (WRC) to drive Arp2/3 complex-mediated actin polymerization in many essential processes. Rac1 binds to WRC at two distinct sites-the ...The Rho-family GTPase Rac1 activates the WAVE regulatory complex (WRC) to drive Arp2/3 complex-mediated actin polymerization in many essential processes. Rac1 binds to WRC at two distinct sites-the A and D sites. Precisely how Rac1 binds and how the binding triggers WRC activation remain unknown. Here we report WRC structures by itself, and when bound to single or double Rac1 molecules, at ~3 Å resolutions by cryogenic-electron microscopy. The structures reveal that Rac1 binds to the two sites by distinct mechanisms, and binding to the A site, but not the D site, drives WRC activation. Activation involves a series of unique conformational changes leading to the release of sequestered WCA (WH2-central-acidic) polypeptide, which stimulates the Arp2/3 complex to polymerize actin. Together with biochemical and cellular analyses, the structures provide a novel mechanistic understanding of how the Rac1-WRC-Arp2/3-actin signaling axis is regulated in diverse biological processes and diseases. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 539.9 KB | Display | ![]() |
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PDB format | ![]() | 429.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 83.2 KB | Display | |
Data in CIF | ![]() | 127.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 26734MC ![]() 7uscC ![]() 7usdC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 5 types, 5 molecules ABCDE
#1: Protein | Mass: 145363.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: This construct contains two additional uncleaved residues "GA" in the N terminus from the construct design and purification procedure. Densities for these residues are not observed in the ...Details: This construct contains two additional uncleaved residues "GA" in the N terminus from the construct design and purification procedure. Densities for these residues are not observed in the map and were not included in the sample sequence to avoid numbering shifts. Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 128940.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: This construct contains two additional uncleaved residues "GA" in the N terminus from the construct design and purification procedure. Densities for these residues are not observed in the ...Details: This construct contains two additional uncleaved residues "GA" in the N terminus from the construct design and purification procedure. Densities for these residues are not observed in the map and were not included in the sample sequence to avoid numbering shifts. Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 37009.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues 231-248 are inserted as a flexible linker sequence. This construct contains two additional uncleaved residues "GA" in the N terminus from the construct design and purification ...Details: Residues 231-248 are inserted as a flexible linker sequence. This construct contains two additional uncleaved residues "GA" in the N terminus from the construct design and purification procedure. Densities for these residues are not observed in the map and were not included in the sample sequence to avoid numbering shifts. Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein | Mass: 8756.915 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: This construct contains uncleaved residues "GHMGAA" in the N terminus from the construct design and purification procedure. Densities for the residues are not observed in the map and were ...Details: This construct contains uncleaved residues "GHMGAA" in the N terminus from the construct design and purification procedure. Densities for the residues are not observed in the map and were not included in the sample sequence to avoid numbering shifts. Source: (gene. exp.) ![]() ![]() ![]() |
#5: Protein | Mass: 18041.482 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The sequence only contains residues 1-158. Also, there are two additional uncleaved residues "GH" in the N terminus from the construct design and purification procedure. Densities for these ...Details: The sequence only contains residues 1-158. Also, there are two additional uncleaved residues "GH" in the N terminus from the construct design and purification procedure. Densities for these residues are not observed in the map and were not included in the sample sequence to avoid numbering shifts. Source: (gene. exp.) ![]() ![]() ![]() |
-Ras-related C3 botulinum toxin substrate ... , 2 types, 2 molecules FG
#6: Protein | Mass: 21025.459 Da / Num. of mol.: 1 / Mutation: P29S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#7: Protein | Mass: 21010.486 Da / Num. of mol.: 1 / Mutation: P29S, Q61L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 3 types, 4 molecules ![](data/chem/img/GNP.gif)
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#8: Chemical | ChemComp-GNP / | ||
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#9: Chemical | #10: Chemical | ChemComp-GTP / | |
-Details
Has ligand of interest | Y |
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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: WAVE regulatory complex with Rac1 bound to A and D sites Type: COMPLEX / Entity ID: #1-#7 / Source: MULTIPLE SOURCES | ||||||||||||
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Molecular weight | Value: 0.38 MDa / Experimental value: NO | ||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||
Source (recombinant) |
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Buffer solution | pH: 7 | ||||||||||||
Specimen | Conc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Details: 15 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | ||||||||||||
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA Details: Data were collected by shifting the stage to target exposure positions. |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 1200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 40 sec. / Electron dose: 41.34 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1285 Details: Each micrograph was acquired as dose-fractionated movies consisting of 62 frames per movie. |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 |
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Processing
EM software |
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CTF correction | Details: Particles were CTF-corrected during projection matching and back projection Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 666417 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 139296 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building |
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