4UM8 Immune System date May 15, 2014
title Crystal Structure Of Alpha V Beta 6
authors X.Dong, T.A.Springer
compound source
Molecule: Integrin Alpha-V
Chain: A, C
Fragment: Headpiece, Residues 31-625
Synonym: Vitronectin Receptor Subunit Alpha, Integrin Alpha
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293s Gnt I- Cell
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcdna 3.1 And Et10

Molecule: Integrin Beta-6
Chain: B, D
Synonym: Integrin Beta 6
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293s Gnt I- Cell
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcdna 3.1 And Et10
symmetry Space Group: C 1 2 1
R_factor 0.238 R_Free 0.281
crystal
cell
length a length b length c angle alpha angle beta angle gamma
184.450 170.010 102.390 90.00 98.68 90.00
method X-Ray Diffractionresolution 2.85 Å
ligand BMA, CA, CAC, CL, MAN, MG, NAG, NI, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceStructural determinants of integrin beta-subunit specificity for latent TGF-beta, Dong X, Hudson NE, Lu C, Springer TA, Nat Struct Mol Biol. 2014 Nov 10. doi: 10.1038/nsmb.2905. PMID:25383667
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (614 Kb) [Save to disk]
  • Biological Unit Coordinates (4um8.pdb1.gz) 301 Kb
  • Biological Unit Coordinates (4um8.pdb2.gz) 303 Kb
  • LPC: Ligand-Protein Contacts for 4UM8
  • CSU: Contacts of Structural Units for 4UM8
  • Structure Factors (619 Kb)
  • Retrieve 4UM8 in mmCIF format [Save to disk]
  • Re-refined 4um8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4UM8 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 4UM8
  • 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 4UM8, from MSDmotif at EBI
  • Fold representative 4um8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4um8_D] [4um8] [4um8_A] [4um8_C] [4um8_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4UM8: [EGF_like] [INB] [Int_alpha] [Integrin_B_tail] [Integrin_b_cyt] [PSI] [VWA ] by SMART
  • Other resources with information on 4UM8
  • Community annotation for 4UM8 at PDBWiki (http://pdbwiki.org)

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