PDBsum entry 1ydi

Go to PDB code: 
protein Protein-protein interface(s) links
Cell adhesion, structural protein PDB id
Protein chains
256 a.a. *
24 a.a. *
Waters ×466
* Residue conservation analysis
PDB id:
Name: Cell adhesion, structural protein
Title: Human vinculin head domain (vh1, 1-258) in complex with human alpha-actinin's vinculin-binding site (residues 731- 760)
Structure: Vinculin isoform vcl. Chain: a. Engineered: yes. Alpha-actinin 4. Chain: b. Synonym: non-muscle alpha-actinin 4, f-actin cross linking protein. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: actn4. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
1.80Å     R-factor:   0.181     R-free:   0.232
Authors: T.Izard
Key ref: P.R.Bois et al. (2005). Structural dynamics of alpha-actinin-vinculin interactions. Mol Cell Biol, 25, 6112-6122. PubMed id: 15988023
23-Dec-04     Release date:   19-Jul-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P18206  (VINC_HUMAN) -  Vinculin
1134 a.a.
256 a.a.
Protein chain
Pfam   ArchSchema ?
O43707  (ACTN4_HUMAN) -  Alpha-actinin-4
911 a.a.
24 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     actin cytoskeleton   1 term 
  Biological process     cell adhesion   1 term 
  Biochemical function     structural molecule activity     1 term  


Mol Cell Biol 25:6112-6122 (2005)
PubMed id: 15988023  
Structural dynamics of alpha-actinin-vinculin interactions.
P.R.Bois, R.A.Borgon, C.Vonrhein, T.Izard.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20865173 L.S.Abraham, H.J.Oh, F.Sancar, J.E.Richmond, and H.Kim (2010).
An alpha-catulin homologue controls neuromuscular function through localization of the dystrophin complex and BK channels in Caenorhabditis elegans.
  PLoS Genet, 6, 0.  
20086044 X.Peng, L.E.Cuff, C.D.Lawton, and K.A.DeMali (2010).
Vinculin regulates cell-surface E-cadherin expression by binding to beta-catenin.
  J Cell Sci, 123, 567-577.  
19523901 J.H.Lee, E.S.Rangarajan, S.D.Yogesha, and T.Izard (2009).
Raver1 interactions with vinculin and RNA suggest a feed-forward pathway in directing mRNA to focal adhesions.
  Structure, 17, 833-842.
PDB codes: 3h2u 3h2v
19441055 K.Jani, and F.Schöck (2009).
Molecular mechanisms of mechanosensing in muscle development.
  Dev Dyn, 238, 1526-1534.  
18591676 J.M.Ferrer, H.Lee, J.Chen, B.Pelz, F.Nakamura, R.D.Kamm, and M.J.Lang (2008).
Measuring molecular rupture forces between single actin filaments and actin-binding proteins.
  Proc Natl Acad Sci U S A, 105, 9221-9226.  
18571811 M.Seimiya, T.Tomonaga, K.Matsushita, M.Sunaga, M.Oh-Ishi, Y.Kodera, T.Maeda, S.Takano, A.Togawa, H.Yoshitomi, M.Otsuka, M.Yamamoto, M.Nakano, M.Miyazaki, and F.Nomura (2008).
Identification of novel immunohistochemical tumor markers for primary hepatocellular carcinoma; clathrin heavy chain and formiminotransferase cyclodeaminase.
  Hepatology, 48, 519-530.  
18408041 S.E.Lee, S.Chunsrivirot, R.D.Kamm, and M.R.Mofrad (2008).
Molecular dynamics study of talin-vinculin binding.
  Biophys J, 95, 2027-2036.  
18851762 T.Y.Chang, Y.Y.Li, C.H.Jen, T.P.Yang, C.H.Lin, M.T.Hsu, and H.W.Wang (2008).
easyExon--a Java-based GUI tool for processing and visualization of Affymetrix exon array data.
  BMC Bioinformatics, 9, 432.  
18282082 V.P.Hytönen, and V.Vogel (2008).
How force might activate talin's vinculin binding sites: SMD reveals a structural mechanism.
  PLoS Comput Biol, 4, e24.  
17932491 G.T.Nhieu, and T.Izard (2007).
Vinculin binding in its closed conformation by a helix addition mechanism.
  EMBO J, 26, 4588-4596.
PDB code: 2ibf
17928215 M.A.Arnaout, S.L.Goodman, and J.P.Xiong (2007).
Structure and mechanics of integrin-based cell adhesion.
  Curr Opin Cell Biol, 19, 495-507.  
16826238 C.Hamiaux, A.van Eerde, C.Parsot, J.Broos, and B.W.Dijkstra (2006).
Structural mimicry for vinculin activation by IpaA, a virulence factor of Shigella flexneri.
  EMBO Rep, 7, 794-799.
PDB code: 2gdc
17192196 P.J.Gardina, T.A.Clark, B.Shimada, M.K.Staples, Q.Yang, J.Veitch, A.Schweitzer, T.Awad, C.Sugnet, S.Dee, C.Davies, A.Williams, and Y.Turpaz (2006).
Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array.
  BMC Genomics, 7, 325.  
17125150 R.L.Rich, and D.G.Myszka (2006).
Survey of the year 2005 commercial optical biosensor literature.
  J Mol Recognit, 19, 478-534.  
17088427 T.Izard, G.Tran Van Nhieu, and P.R.Bois (2006).
Shigella applies molecular mimicry to subvert vinculin and invade host cells.
  J Cell Biol, 175, 465-475.
PDB codes: 2gww 2hsq
16893648 W.H.Ziegler, R.C.Liddington, and D.R.Critchley (2006).
The structure and regulation of vinculin.
  Trends Cell Biol, 16, 453-460.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.