Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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: 32.43 kDa 
• Atom Count: 2725 
• Modelled Residue Count: 280 
• Deposited Residue Count: 287 
• Unique protein chains: 2

1YDI

Human Vinculin Head Domain (VH1, 1-258) in Complex with Human Alpha-Actinin's Vinculin-Binding Site (Residues 731-760)

• PDB DOI: 10.2210/pdb1YDI/pdb

• Classification: Cell Adhesion, Structural Protein
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-12-23 Released: 2005-07-19 
• Deposition Author(s): Izard, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.232 
• R-Value Work: 0.171 
• R-Value Observed: 0.181 

Literature

Structural Dynamics of {alpha}-Actinin-Vinculin Interactions.

Bois, P.R., Borgon, R.A., Vonrhein, C., Izard, T.

(2005) Mol Cell Biol 14: 6112-6122

• PubMed: 15988023 
• DOI: 10.1128/MCB.25.14.6112-6122.2005
• Primary Citation of Related Structures:  
  1YDI


• PubMed Abstract: 
  

Alpha-actinin and vinculin orchestrate reorganization of the actin cytoskeleton following the formation of adhesion junctions. alpha-Actinin interacts with vinculin through the binding of an alpha-helix (alphaVBS) present within the R4 spectrin repeat of its central rod domain to vinculin's N-terminal seven-helical bundle domain (Vh1). The Vh1:alphaVBS structure suggests that alphaVBS first unravels from its buried location in the triple-helical R4 repeat to allow it to bind to vinculin. alphaVBS binding then induces novel conformational changes in the N-terminal helical bundle of Vh1, which disrupt its intramolecular association with vinculin's tail domain and which differ from the alterations in Vh1 provoked by the binding of talin. Surprisingly, alphaVBS binds to Vh1 in an inverted orientation compared to the binding of talin's VBSs to vinculin. Importantly, the binding of alphaVBS and talin's VBSs to vinculin's Vh1 domain appear to also trigger distinct conformational changes in full-length vinculin, opening up distant regions that are buried in the inactive molecule. The data suggest a model where vinculin's Vh1 domain acts as a molecular switch that undergoes distinct structural changes provoked by talin and alpha-actinin binding in focal adhesions versus adherens junctions, respectively.

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Organizational Affiliation: 

Department of Hematology-Oncology, St. Jude Children's Research Hospital, 332 North Lauderdale Street, Memphis, Tennessee 38105, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
vinculin isoform VCL	A	263	Homo sapiens	Mutation(s): 0  Gene Names: VCL
UniProt & NIH Common Fund Data Resources
Find proteins for P18206 (Homo sapiens) Explore P18206  Go to UniProtKB:  P18206
PHAROS:  P18206 GTEx:  ENSG00000035403

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-actinin 4	B	24	Homo sapiens	Mutation(s): 0  Gene Names: ACTN4
UniProt & NIH Common Fund Data Resources
Find proteins for O43707 (Homo sapiens) Explore O43707  Go to UniProtKB:  O43707
PHAROS:  O43707 GTEx:  ENSG00000130402

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.232 
• R-Value Work: 0.171 
• R-Value Observed: 0.181 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.843	α = 90
b = 54.268	β = 107.57
c = 63.598	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-12-23 
• Released Date: 2005-07-19 
Deposition Author(s): Izard, T.

Revision History  

• Version 1.0: 2005-07-19
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance