9JW0 | pdb_00009jw0

Structure of the N-terminal 3 domains (V1-V3) villin bound to actin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 
    0.259 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.204 (DCC) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

The structure of an actin nucleus stabilized by villin.

Robinson, R.C.Chongrungreang, T.Ponlachantra, K.Boonyarit, B.Dilly, G.F.Li, Y.I.Girguis, P.R.Copley, R.R.Claridge-Chang, A.

(2025) Sci Adv 11: eadw6915-eadw6915

  • DOI: https://doi.org/10.1126/sciadv.adw6915
  • Primary Citation of Related Structures:  
    9JUS, 9JVT, 9JW0

  • PubMed Abstract: 

    Villin is an actin filament nucleating, severing, capping and bundling protein; however, the structural basis for villin's functions and the characteristics of the actin polymerization nucleus remain poorly understood. Here, we present the structure of vent-worm villin bound to a trimeric actin nucleus. Villin wraps around and caps the barbed end of the actin trimer. Its headpiece domain interacts at the junction of two laterally associated actin protomers, leaving the pointed-end subunits open for elongation. Within the actin trimer, the two longitudinally associated subunits adopt barbed and pointed-end subunit conformations, while the lateral protomer exhibits a monomeric conformation. This provides the first view of an actin-filament nucleus, revealing that the transition into the filamentous form is stimulated and stabilized by the interactions with the pointed-end subunits. Our results also illuminate mechanisms of actin-filament dynamics and villin capping and severing, suggesting that F-to-G actin conformational transitions facilitate the later process.


  • Organizational Affiliation
    • School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210 Thailand.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Villin400Paralvinella sulfincolaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, alpha skeletal muscle377Gallus gallusMutation(s): 0 
Gene Names: ACTA1ACTA
EC: 3.6.4
UniProt
Find proteins for P68139 (Gallus gallus)
Explore P68139 
Go to UniProtKB:  P68139
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68139
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free:  0.259 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.204 (DCC) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.71α = 90
b = 93.762β = 90
c = 114.323γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited StatesMoore-Simons GBMF9743
Human Frontier Science Program (HFSP)FranceRGP0028/2018

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-15
    Type: Initial release
  • Version 1.1: 2025-12-17
    Changes: Database references