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- PDB-6yw7: Cryo-EM structure of the ARP2/3 1A5C isoform complex. -

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Basic information

Entry
Database: PDB / ID: 6yw7
TitleCryo-EM structure of the ARP2/3 1A5C isoform complex.
Components(Actin-related protein ...) x 7
KeywordsSTRUCTURAL PROTEIN / Cytoskeleton
Function / homology
Function and homology information


meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / spindle localization / meiotic cytokinesis / actin polymerization-dependent cell motility / muscle cell projection membrane / asymmetric cell division / Arp2/3 protein complex / actin nucleation ...meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / spindle localization / meiotic cytokinesis / actin polymerization-dependent cell motility / muscle cell projection membrane / asymmetric cell division / Arp2/3 protein complex / actin nucleation / Arp2/3 complex-mediated actin nucleation / actin cap / regulation of actin filament polymerization / positive regulation of actin filament polymerization / filamentous actin / establishment or maintenance of cell polarity / brush border / cilium assembly / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / positive regulation of double-strand break repair via homologous recombination / positive regulation of lamellipodium assembly / actin filament polymerization / EPHB-mediated forward signaling / positive regulation of substrate adhesion-dependent cell spreading / cell projection / FCGR3A-mediated phagocytosis / cellular response to nerve growth factor stimulus / Regulation of actin dynamics for phagocytic cup formation / cellular response to type II interferon / structural constituent of cytoskeleton / actin filament binding / azurophil granule lumen / cell-cell junction / synaptic vesicle membrane / cell migration / lamellipodium / actin cytoskeleton / Clathrin-mediated endocytosis / site of double-strand break / actin binding / actin cytoskeleton organization / secretory granule lumen / cell cortex / ficolin-1-rich granule lumen / postsynapse / neuron projection / endosome / focal adhesion / Neutrophil degranulation / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Actin-related protein 2/3 complex subunit 5 / ARP2/3 complex 16 kDa subunit (p16-Arc) / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 1 / Arp2/3 complex subunit 2/4 / Actin-related protein 2/3 complex subunit 5 superfamily / Actin-related protein 2/3 complex subunit 3 superfamily / Arp2/3 complex, 34 kD subunit p34-Arc ...Actin-related protein 2/3 complex subunit 5 / ARP2/3 complex 16 kDa subunit (p16-Arc) / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 1 / Arp2/3 complex subunit 2/4 / Actin-related protein 2/3 complex subunit 5 superfamily / Actin-related protein 2/3 complex subunit 3 superfamily / Arp2/3 complex, 34 kD subunit p34-Arc / ARP2/3 complex ARPC3 (21 kDa) subunit / ARP2/3 complex 20 kDa subunit (ARPC4) / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 5 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 3 / Actin-related protein 2 / Actin-related protein 2/3 complex subunit 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
Authorsvon Loeffelholz, O. / Moores, C. / Purkiss, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L00190X/1 United Kingdom
CitationJournal: 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
DepositionApr 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Actin-related protein 3
D: Actin-related protein 2/3 complex subunit 2
E: Actin-related protein 2/3 complex subunit 3
B: Actin-related protein 2
F: Actin-related protein 2/3 complex subunit 4
G: Actin-related protein 2/3 complex subunit 5
C: Actin-related protein 2/3 complex subunit 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,8839
Polymers224,8687
Non-polymers1,0142
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Actin-related protein ... , 7 types, 7 molecules ADEBFGC

#1: Protein Actin-related protein 3 / Actin-like protein 3


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
#2: Protein Actin-related protein 2/3 complex subunit 2 / Arp2/3 complex 34 kDa subunit / p34-ARC


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 Actin-related protein 2/3 complex subunit 3 / Arp2/3 complex 21 kDa subunit / p21-ARC


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 Actin-related protein 2 / Actin-like protein 2


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 Actin-related protein 2/3 complex subunit 4 / Arp2/3 complex 20 kDa subunit / p20-ARC


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 Actin-related protein 2/3 complex subunit 5 / Arp2/3 complex 16 kDa subunit / p16-ARC


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 Actin-related protein 2/3 complex subunit 1A / SOP2-like 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

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Non-polymers , 1 types, 2 molecules

#8: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human ARP2/3 1A5C isoform complex / Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 59 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 130973 / Symmetry type: POINT

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