7T5Q | pdb_00007t5q

Cryo-EM Structure of a Transition State of Arp2/3 Complex Activation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Transition State of Arp2/3 Complex Activation by Actin-Bound Dimeric Nucleation-Promoting Factor.

van Eeuwen, T.Boczkowska, M.Rebowski, G.Carman, P.J.Fregoso, F.E.Dominguez, R.

(2023) Proc Natl Acad Sci U S A 120: e2306165120-e2306165120

  • DOI: https://doi.org/10.1073/pnas.2306165120
  • Primary Citation of Related Structures:  
    7T5Q

  • PubMed Abstract: 

    Arp2/3 complex generates branched actin networks that drive fundamental processes such as cell motility and cytokinesis. The complex comprises seven proteins, including actin-related proteins (Arps) 2 and 3 and five scaffolding proteins (ArpC1-ArpC5) that mediate interactions with a pre-existing (mother) actin filament at the branch junction. Arp2/3 complex exists in two main conformations, inactive with the Arps interacting end-to-end and active with the Arps interacting side-by-side like subunits of the short-pitch helix of the actin filament. Several cofactors drive the transition toward the active state, including ATP binding to the Arps, WASP-family nucleation-promoting factors (NPFs), actin monomers, and binding of Arp2/3 complex to the mother filament. The precise contribution of each cofactor to activation is poorly understood. We report the 3.32-Å resolution cryo-electron microscopy structure of a transition state of Arp2/3 complex activation with bound constitutively dimeric NPF. Arp2/3 complex-binding region of the NPF N-WASP was fused C-terminally to the α and β subunits of the CapZ heterodimer. One arm of the NPF dimer binds Arp2 and the other binds actin and Arp3. The conformation of the complex is intermediate between those of inactive and active Arp2/3 complex. Arp2, Arp3, and actin also adopt intermediate conformations between monomeric (G-actin) and filamentous (F-actin) states, but only actin hydrolyzes ATP. In solution, the transition complex is kinetically shifted toward the short-pitch conformation and has higher affinity for F-actin than inactive Arp2/3 complex. The results reveal how all the activating cofactors contribute in a coordinated manner toward Arp2/3 complex activation.


  • Organizational Affiliation
    • Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 3418Bos taurusMutation(s): 0 
UniProt
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UniProt GroupP61157
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2394Bos taurusMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 1A370Bos taurusMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 2300Bos taurusMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 3178Bos taurusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 4168Bos taurusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 5151Bos taurusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, alpha skeletal muscle375Oryctolagus cuniculusMutation(s): 0 
EC: 3.6.4
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
F-actin-capping protein subunit alpha-1/Actin nucleation-promoting factor WASL chimera346Homo sapiensMus musculus
This entity is chimeric
Mutation(s): 0 
Gene Names: CAPZA1Wasl
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GTEx:  ENSG00000116489 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
F-actin-capping protein subunit beta/Actin nucleation-promoting factor WASL chimera333Homo sapiensMus musculus
This entity is chimeric
Mutation(s): 0 
Gene Names: CAPZBWasl
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GTEx:  ENSG00000077549 
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Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC
H
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM07391
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32-GM008275
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesF31-HL146077

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2023-08-02
    Changes: Structure summary
  • Version 1.2: 2024-10-23
    Changes: Data collection, Database references, Refinement description, Structure summary