1YDI Cell Adhesion, Structural Protein date Dec 23, 2004
title Human Vinculin Head Domain (Vh1, 1-258) In Complex With Human Alpha-Actinin'S Vinculin-Binding Site (Residues 731- 760)
authors T.Izard
compound source
Molecule: Vinculin Isoform Vcl
Chain: A
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3

Molecule: Alpha-Actinin 4
Chain: B
Synonym: Non-Muscle Alpha-Actinin 4, F-Actin Cross Linking Protein;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Actn4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.171 R_Free 0.232
crystal
cell
length a length b length c angle alpha angle beta angle gamma
42.843 54.268 63.598 90.00 107.57 90.00
method X-Ray Diffractionresolution 1.80 Å
Primary referenceStructural Dynamics of {alpha}-Actinin-Vinculin Interactions., Bois PR, Borgon RA, Vonrhein C, Izard T, Mol Cell Biol 2005 Jul;25(14):6112-22. PMID:15988023
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (58 Kb) [Save to disk]
  • Biological Unit Coordinates (1ydi.pdb1.gz) 55 Kb
  • CSU: Contacts of Structural Units for 1YDI
  • Likely Quarternary Molecular Structure file(s) for 1YDI
  • Retrieve 1YDI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YDI from S2C, [Save to disk]
  • View 1YDI 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 1YDI
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1YDI, from MSDmotif at EBI
  • Fold representative 1ydi from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ydi_B] [1ydi] [1ydi_A]
  • SWISS-PROT database: [O43707] [P18206]
  • Domain organization of [ACTN4_HUMAN] [VINC_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 1YDI with the sequences similar proteins can be viewed for 1YDI's classification [ACTN4_HUMAN] [VINC_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [ACTN4_HUMAN] [VINC_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1YDI
  • Community annotation for 1YDI at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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