4DJ9 Cell Adhesion date Feb 01, 2012
title Human Vinculin Head Domain Vh1 (Residues 1-258) In Complex W Talin Vinculin Binding Site 50 (Vbs50, Residues 2078-2099)
authors S.D.Yogesha, E.S.Rangarajan, C.Vonrhein, G.Bricogne, T.Izard
compound source
Molecule: Vinculin
Chain: A
Fragment: Unp Residues 1-258
Synonym: Metavinculin
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Vcl

Molecule: Talin-1
Chain: B
Fragment: Unp Residues 2075-2103
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tln1, Kiaa1027, Tln
symmetry Space Group: P 21 21 21
R_factor 0.208 R_Free 0.247
length a length b length c angle alpha angle beta angle gamma
33.540 68.160 137.600 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.25 Å

Primary referenceCrystal structure of vinculin in complex with vinculin binding site 50 (VBS50), the integrin binding site 2 (IBS2) of talin., Yogesha SD, Rangarajan ES, Vonrhein C, Bricogne G, Izard T, Protein Sci. 2012 Feb 14. doi: 10.1002/pro.2041. PMID:22334306
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (92 Kb) [Save to disk]
  • Biological Unit Coordinates (4dj9.pdb1.gz) 88 Kb
  • CSU: Contacts of Structural Units for 4DJ9
  • Structure Factors (278 Kb)
  • Retrieve 4DJ9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DJ9 from S2C, [Save to disk]
  • Re-refined 4dj9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DJ9 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4DJ9
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4DJ9, from MSDmotif at EBI
  • Fold representative 4dj9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dj9_A] [4dj9_B] [4dj9]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4DJ9
  • Community annotation for 4DJ9 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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