+Open data
-Basic information
Entry | Database: PDB / ID: 7usc | ||||||
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Title | Cryo-EM structure of WAVE Regulatory Complex | ||||||
Components |
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Keywords | CELL INVASION / actin regulator / GTPase binding protein / cytoskeletal regulator | ||||||
Function / homology | Function and homology information 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 / dendrite extension / regulation of translation at postsynapse, modulating synaptic transmission / filopodium tip / regulation of modification of postsynaptic actin cytoskeleton / regulation of actin filament polymerization / RNA 7-methylguanosine cap binding / ruffle organization / cell projection assembly / axon extension / positive regulation of ruffle assembly / positive regulation of dendrite development / lamellipodium assembly / regulation of myelination / protein kinase A binding / cortical actin cytoskeleton organization / positive regulation of actin filament polymerization / Rac protein signal transduction / protein kinase A regulatory subunit binding / filamentous actin / dendritic growth cone / lamellipodium membrane / excitatory synapse / RHOG GTPase cycle / RAC2 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / positive regulation of axon extension / axonal growth cone / positive regulation of lamellipodium assembly / neuron projection morphogenesis / response to electrical stimulus / translation repressor activity / ruffle / cellular response to brain-derived neurotrophic factor stimulus / RAC1 GTPase cycle / actin filament polymerization / receptor-mediated endocytosis / mitochondrion organization / filopodium / central nervous system development / actin filament organization / axon guidance / cell motility / FCGR3A-mediated phagocytosis / positive regulation of protein-containing complex assembly / cell morphogenesis / terminal bouton / cellular response to insulin stimulus / Regulation of actin dynamics for phagocytic cup formation / cognition / small GTPase binding / VEGFA-VEGFR2 Pathway / positive regulation of fibroblast proliferation / actin filament binding / specific granule lumen / actin cytoskeleton / cell migration / tertiary granule lumen / lamellipodium / regulation of translation / actin binding / regulation of cell shape / fibroblast proliferation / actin cytoskeleton organization / protein-containing complex assembly / secretory granule lumen / in utero embryonic development / mitochondrial outer membrane / postsynapse / dendritic spine / cytoskeleton / neuron projection / intracellular membrane-bounded organelle / focal adhesion / neuronal cell body / synapse / Neutrophil degranulation / protein-containing complex binding / apoptotic process / perinuclear region of cytoplasm / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Ding, B. / Yang, S. / Chen, B. / Chowdhury, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7usc.cif.gz | 486.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7usc.ent.gz | 389.1 KB | Display | PDB format |
PDBx/mmJSON format | 7usc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7usc_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7usc_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7usc_validation.xml.gz | 74.9 KB | Display | |
Data in CIF | 7usc_validation.cif.gz | 116.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/us/7usc ftp://data.pdbj.org/pub/pdb/validation_reports/us/7usc | HTTPS FTP |
-Related structure data
Related structure data | 26732MC 7usdC 7useC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#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.) Homo sapiens (human) / Gene: CYFIP1, KIAA0068 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q7L576 |
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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.) Homo sapiens (human) / Gene: NCKAP1, HEM2, KIAA0587, NAP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y2A7 |
#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.) Homo sapiens (human) / Gene: WASF1, KIAA0269, SCAR1, WAVE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92558 |
#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.) Homo sapiens (human) / Gene: BRK1, C3orf10, HSPC300, MDS027 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WUW1 |
#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.) Homo sapiens (human) / Gene: ABI2 / Production host: Escherichia coli (E. coli) / References: UniProt: E9PEZ7 |
-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: WAVE regulatory complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES | ||||||||||||
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Molecular weight | Value: 0.34 MDa / Experimental value: NO | ||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||
Source (recombinant) |
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Buffer solution | pH: 7 | ||||||||||||
Specimen | Conc.: 0.41 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Details: 30 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 |
-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 the target exposure positions. |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 1200 nm / Nominal defocus min: 600 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: 44.06 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2913 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 |
-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: 2006821 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 95319 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building |
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