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- PDB-9dlz: Bovine Arp2/3 complex with N-WASP CA bound to Arp3 -

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Basic information

Entry
Database: PDB / ID: 9dlz
TitleBovine Arp2/3 complex with N-WASP CA bound to Arp3
Components
  • (Actin-related protein ...) x 7
  • WASP like actin nucleation promoting factor
KeywordsSTRUCTURAL PROTEIN / actin / arp 2-3 complex / N-WASP / nucleation promoting factor
Function / homology
Function and homology information


muscle cell projection membrane / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / regulation of actin filament polymerization / Clathrin-mediated endocytosis / Neutrophil degranulation / positive regulation of actin filament polymerization ...muscle cell projection membrane / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / regulation of actin filament polymerization / Clathrin-mediated endocytosis / Neutrophil degranulation / positive regulation of actin filament polymerization / cilium assembly / positive regulation of double-strand break repair via homologous recombination / positive regulation of lamellipodium assembly / actin filament polymerization / positive regulation of substrate adhesion-dependent cell spreading / actin filament organization / cell projection / structural constituent of cytoskeleton / actin filament binding / synaptic vesicle membrane / cell migration / site of double-strand break / lamellipodium / actin binding / cell cortex / cytoskeleton / neuron projection / postsynapse / endosome / focal adhesion / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / 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 nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / 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) / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / WH2 domain profile. / WH2 domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / PH-like domain superfamily / 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 / WASP like actin nucleation promoting factor / Actin-related protein 2 / Actin-related protein 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 1A / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 5 / Actin-related protein 2/3 complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSaks, A.J. / Barrie, K.R. / Dominguez, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM073791-19 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: NPF binding to Arp2 is allosterically linked to the release of ArpC5's N-terminal tail and conformational changes in Arp2/3 complex.
Authors: Andrew J Saks / Kyle R Barrie / Grzegorz Rebowski / Roberto Dominguez /
Abstract: Arp2/3 complex generates branched actin networks essential for numerous motile functions of the cell. It comprises seven subunits: actin-related proteins (Arps) 2 and 3 and five scaffolding subunits ...Arp2/3 complex generates branched actin networks essential for numerous motile functions of the cell. It comprises seven subunits: actin-related proteins (Arps) 2 and 3 and five scaffolding subunits (ArpC1-5). The complex adopts two major conformations: inactive, with the Arps interacting end-to-end, and active, with the Arps aligned side-by-side like subunits in the actin filament. Activation involves several cofactors, including ATP, WASP-family nucleation-promoting factors (NPFs), actin monomers, and the mother actin filament. NPFs bind to two sites, one on Arp2-ArpC1 and one on Arp3, delivering actin subunits at the barbed end of the Arps to initiate branch elongation. However, the mechanisms by which each NPF drives the equilibrium toward activation remain unclear. We present two cryo-electron microscopy (cryo-EM) structures of Arp2/3 complex at 2.9-Å resolution: one with NPFs bound to Arp3 and ArpC1 but not Arp2 and another with NPFs bound to Arp3 and Arp2-ArpC1. The structures reveal that NPF binding to Arp2 is allosterically linked to the release of ArpC5's N-terminal tail from Arp2 and conformational changes in Arp2, including closure of its ATP-binding cleft and partial rotation and translation toward its position in the active complex at the branch. Previous work identified another allosteric switch linking NPF binding to Arp3 with the release of its inhibitory C-terminal tail, which we also observe. In summary, both NPF-binding sites induce allosteric changes in Arp2/3 complex, collectively shifting the equilibrium toward activation.
History
DepositionSep 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin-related protein 3
B: Actin-related protein 2
C: Actin-related protein 2/3 complex subunit 1A
D: Actin-related protein 2/3 complex subunit 2
E: Actin-related protein 2/3 complex subunit 3
F: Actin-related protein 2/3 complex subunit 4
G: Actin-related protein 2/3 complex subunit 5
H: WASP like actin nucleation promoting factor
I: WASP like actin nucleation promoting factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,36613
Polymers230,3039
Non-polymers1,0634
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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

#1: Protein Actin-related protein 3 / Actin-2 / Actin-like protein 3


Mass: 46704.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P61157
#2: Protein Actin-related protein 2 / Actin-like protein 2


Mass: 44362.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: A7MB62
#3: Protein Actin-related protein 2/3 complex subunit 1A


Mass: 41594.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q1JP79
#4: Protein Actin-related protein 2/3 complex subunit 2 / Arp2/3 complex 34 kDa subunit / p34-ARC


Mass: 32672.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q3MHR7
#5: Protein Actin-related protein 2/3 complex subunit 3 / Arp2/3 complex 21 kDa subunit / p21-ARC


Mass: 20256.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q3T035
#6: Protein Actin-related protein 2/3 complex subunit 4 / Arp2/3 complex 20 kDa subunit / p20-ARC


Mass: 19565.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q148J6
#7: Protein Actin-related protein 2/3 complex subunit 5 / Arp2/3 complex 16 kDa subunit / p16-ARC


Mass: 15589.517 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q3SYX9

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Protein/peptide , 1 types, 2 molecules HI

#8: Protein/peptide WASP like actin nucleation promoting factor


Mass: 4778.878 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: mPipKuh1_018740 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7J7WN29

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Non-polymers , 2 types, 4 molecules

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


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
Has protein modificationN

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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: Arp 2/3 complex bound to NPFs / Type: COMPLEX / Entity ID: #3-#8 / Source: NATURAL
Molecular weightValue: 0.22 MDa / Experimental value: YES
Source (natural)Organism: Bos taurus (domestic cattle)
Buffer solutionpH: 7.4
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 47 e/Å2 / Film or detector model: OTHER

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 292625 / Symmetry type: POINT

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