9JW0 | pdb_00009jw0

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

• PDB DOI: https://doi.org/10.2210/pdb9JW0/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Paralvinella sulfincola, Gallus gallus
• Expression System: Escherichia coli, Gallus gallus
• Mutation(s): No 


• Deposited: 2024-10-09 Released: 2025-10-15 
• Deposition Author(s): Robinson, R.C.
• Funding Organization(s): Other private, Human Frontier Science Program (HFSP)

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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

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

• PubMed: 41337577 
• DOI: https://doi.org/10.1126/sciadv.adw6915
• Primary Citation 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.

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Organizational Affiliation: 
• School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210 Thailand.
Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama 700-8530, Japan.
School of Information Science and Technology (IST), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand.
Department of Biology, California State University Channel Islands, 1 University Drive, Camarillo, CA 93012, USA.
Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA.
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Sorbonne Université, Villefranche-sur-Mer, France.
Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore 138673, Singapore.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 88.05 kDa 
• Atom Count: 5,731 
• Modeled Residue Count: 706 
• Deposited Residue Count: 777 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Villin	A	400	Paralvinella sulfincola	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	B	377	Gallus gallus	Mutation(s): 0  Gene Names: ACTA1, ACTA EC: 3.6.4
UniProt
Find proteins for P68139 (Gallus gallus) Explore P68139  Go to UniProtKB:  P68139

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	G [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CA (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A], F [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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 = 84.71	α = 90
b = 93.762	β = 90
c = 114.323	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-15 
Deposition Author(s): Robinson, R.C.

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Funding Organization	Location	Grant Number
Other private	United States	Moore-Simons GBMF9743
Human Frontier Science Program (HFSP)	France	RGP0028/2018

Revision History  

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