1RKE Cell Adhesion, Structural Protein date Nov 21, 2003
title Human Vinculin Head (1-258) In Complex With Human Vinculin Tail (879-1066)
authors T.Izard, G.Evans, R.A.Borgon, C.L.Rush, G.Bricogne, P.R.Bois
compound source
Molecule: Vinculin
Chain: A
Fragment: Vinculin Head (Residues 1-258)
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Vcl
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid

Molecule: Vcl Protein
Chain: B
Fragment: Vinculin Tail (Residues 879-1066)
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
symmetry Space Group: P 21 21 2
R_factor 0.206 R_Free 0.278
crystal
cell
length a length b length c angle alpha angle beta angle gamma
86.603 161.648 36.040 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.35 Å
related structures by homologous chain: 1QKR, 1T01, 1U6H
Primary referenceVinculin activation by talin through helical bundle conversion., Izard T, Evans G, Borgon RA, Rush CL, Bricogne G, Bois PR, Nature 2004 Jan 8;427(6970):171-5. Epub 2003 Dec 31. PMID:14702644
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (1rke.pdb1.gz) 74 Kb
  • CSU: Contacts of Structural Units for 1RKE
  • Likely Quarternary Molecular Structure file(s) for 1RKE
  • Retrieve 1RKE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RKE from S2C, [Save to disk]
  • View 1RKE 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 1RKE
  • 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 1RKE, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1rkea1, region A:-3-128 [Jmol] [rasmolscript] [script source]
        - Domain d1rkea2, region A:129-258 [Jmol] [rasmolscript] [script source]
        - Domain d1rkeb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1rke from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1rke_B] [1rke_A] [1rke]
  • SWISS-PROT database: [P18206]
  • Domain organization of [VINC_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 1RKE with the sequences similar proteins can be viewed for 1RKE's classification [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 [VINC_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1RKE
  • Community annotation for 1RKE 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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