+Open data
-Basic information
Entry | Database: PDB / ID: 6yw7 | ||||||
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Title | Cryo-EM structure of the ARP2/3 1A5C isoform complex. | ||||||
Components | (Actin-related protein ...) x 7 | ||||||
Keywords | STRUCTURAL PROTEIN / Cytoskeleton | ||||||
Function / homology | Function and homology information meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / muscle cell projection membrane / meiotic cytokinesis / spindle localization / actin polymerization-dependent cell motility / Arp2/3 protein complex / asymmetric cell division / Arp2/3 complex-mediated actin nucleation ...meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / muscle cell projection membrane / meiotic cytokinesis / spindle localization / actin polymerization-dependent cell motility / Arp2/3 protein complex / asymmetric cell division / Arp2/3 complex-mediated actin nucleation / actin nucleation / actin cap / regulation of actin filament polymerization / membrane organization / establishment or maintenance of cell polarity / positive regulation of actin filament polymerization / Fc-gamma receptor signaling pathway involved in phagocytosis / filamentous actin / brush border / cilium assembly / positive regulation of double-strand break repair via homologous recombination / ephrin receptor signaling pathway / RHO GTPases Activate WASPs and WAVEs / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / EPHB-mediated forward signaling / actin filament polymerization / cellular response to nerve growth factor stimulus / cell projection / FCGR3A-mediated phagocytosis / structural constituent of cytoskeleton / cellular response to type II interferon / Regulation of actin dynamics for phagocytic cup formation / azurophil granule lumen / cell-cell junction / actin filament binding / actin cytoskeleton / cell migration / lamellipodium / Clathrin-mediated endocytosis / site of double-strand break / actin binding / cell cortex / actin cytoskeleton organization / secretory granule lumen / ficolin-1-rich granule lumen / endosome / neuron projection / focal adhesion / glutamatergic synapse / Neutrophil degranulation / enzyme binding / positive regulation of transcription by RNA polymerase II / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | ||||||
Authors | von Loeffelholz, O. / Moores, C. / Purkiss, A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Biol Open / Year: 2020 Title: Cryo-EM of human Arp2/3 complexes provides structural insights into actin nucleation modulation by ARPC5 isoforms. Authors: Ottilie von Loeffelholz / Andrew Purkiss / Luyan Cao / Svend Kjaer / Naoko Kogata / Guillaume Romet-Lemonne / Michael Way / Carolyn A Moores / Abstract: The Arp2/3 complex regulates many cellular processes by stimulating formation of branched actin filament networks. Because three of its seven subunits exist as two different isoforms, mammals produce ...The Arp2/3 complex regulates many cellular processes by stimulating formation of branched actin filament networks. Because three of its seven subunits exist as two different isoforms, mammals produce a family of Arp2/3 complexes with different properties that may be suited to different physiological contexts. To shed light on how isoform diversification affects Arp2/3 function, we determined a 4.2 Å resolution cryo-EM structure of the most active human Arp2/3 complex containing ARPC1B and ARPC5L, and compared it with the structure of the least active ARPC1A-ARPC5-containing complex. The architecture of each isoform-specific Arp2/3 complex is the same. Strikingly, however, the N-terminal half of ARPC5L is partially disordered compared to ARPC5, suggesting that this region of ARPC5/ARPC5L is an important determinant of complex activity. Confirming this idea, the nucleation activity of Arp2/3 complexes containing hybrid ARPC5/ARPC5L subunits is higher when the ARPC5L N-terminus is present, thereby providing insight into activity differences between the different Arp2/3 complexes. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6yw7.cif.gz | 230.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yw7.ent.gz | 123.5 KB | Display | PDB format |
PDBx/mmJSON format | 6yw7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yw7_validation.pdf.gz | 1023.9 KB | Display | wwPDB validaton report |
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Full document | 6yw7_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6yw7_validation.xml.gz | 43.2 KB | Display | |
Data in CIF | 6yw7_validation.cif.gz | 71.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/6yw7 ftp://data.pdbj.org/pub/pdb/validation_reports/yw/6yw7 | HTTPS FTP |
-Related structure data
Related structure data | 10960MC 6yw6C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Actin-related protein ... , 7 types, 7 molecules ADEBFGC
#1: Protein | Mass: 47428.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACTR3, ARP3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P61158 |
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#2: Protein | Mass: 34386.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARPC2, ARC34, PRO2446 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O15144 |
#3: Protein | Mass: 20572.666 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARPC3, ARC21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O15145 |
#4: Protein | Mass: 44818.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACTR2, ARP2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P61160 |
#5: Protein | Mass: 19697.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARPC4, ARC20 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59998 |
#6: Protein | Mass: 16341.407 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARPC5, ARC16 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O15511 |
#7: Protein | Mass: 41624.262 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARPC1A, SOP2L / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92747 |
-Non-polymers , 1 types, 2 molecules
#8: Chemical |
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-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 |
-Sample preparation
Component | Name: human ARP2/3 1A5C isoform complex / Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 59 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 130973 / Symmetry type: POINT |