3VI3 Cell Adhesion Immune System date Sep 21, 2011
title Crystal Structure Of Alpha5beta1 Integrin Headpiece (Ligand-
authors M.Nagae, T.Nogi, J.Takagi
compound source
Molecule: Integrin Alpha-5
Chain: A, C
Fragment: Unp Residues 42-664
Synonym: Cd49 Antigen-Like Family Member E, Fibronectin Rec Subunit Alpha, Integrin Alpha-F, Vla-5, Integrin Alpha-5 He Integrin Alpha-5 Light Chain;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Fnra, Itga5
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell: Cho-Lec3.2.8.1 Cell

Molecule: Integrin Beta-1
Chain: B, D
Fragment: Unp Residues 21-465
Synonym: Fibronectin Receptor Subunit Beta, Vla-4 Subunit B
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Fnrb, Itgb1, Mdf2, Msk12
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell: Cho-Lec3.2.8.1 Cell

Molecule: Sg19 Fab Fragment (Light Chain)
Chain: L, E
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Expression_system: Mus Musculus
Expression_system_common: Mouse
Expression_system_taxid: 10090
Expression_system_cell: Hybridoma

Molecule: Sg19 Fab Fragment (Heavy Chain)
Chain: H, F
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Expression_system: Mus Musculus
Expression_system_common: Mouse
Expression_system_taxid: 10090
Expression_system_cell: Hybridoma
symmetry Space Group: P 1
R_factor 0.207 R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
92.956 102.805 125.079 76.10 70.19 71.28
method X-Ray Diffractionresolution 2.90 Å
ligand BMA, CA, MAN, MG, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceCrystal structure of alpha5beta1 integrin ectodomain: Atomic details of the fibronectin receptor., Nagae M, Re S, Mihara E, Nogi T, Sugita Y, Takagi J, J Cell Biol. 2012 Apr 2;197(1):131-40. Epub 2012 Mar 26. PMID:22451694
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (475 Kb) [Save to disk]
  • Biological Unit Coordinates (3vi3.pdb1.gz) 238 Kb
  • Biological Unit Coordinates (3vi3.pdb2.gz) 236 Kb
  • LPC: Ligand-Protein Contacts for 3VI3
  • CSU: Contacts of Structural Units for 3VI3
  • Structure Factors (2214 Kb)
  • Retrieve 3VI3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VI3 from S2C, [Save to disk]
  • Re-refined 3vi3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3VI3 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 3VI3
  • 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 3VI3, from MSDmotif at EBI
  • Fold representative 3vi3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vi3_A] [3vi3_B] [3vi3_D] [3vi3_C] [3vi3_E] [3vi3_F] [3vi3_H] [3vi3_L] [3vi3]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3VI3: [IG_like] [IGv] [INB] [Int_alpha] [PSI] [VWA ] by SMART
  • Other resources with information on 3VI3
  • Community annotation for 3VI3 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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