4UM9 Immune System date May 15, 2014
title Crystal Structure Of Alpha V Beta 6 With Peptide
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
Synonym: Integrin Beta 6
Engineered: 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: D
Synonym: Integrin Beta 6
Engineered: 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: Transforming Growth Factor Beta 3
Chain: E, F
Fragment: Residues 7-17
Engineered: 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 0.222 R_Free 0.266
crystal
cell
length a length b length c angle alpha angle beta angle gamma
185.020 168.090 101.800 90.00 98.95 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand ACE, BMA, CA, MAN, MG, NAG, NHH, 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] (626 Kb) [Save to disk]
  • Biological Unit Coordinates (4um9.pdb1.gz) 311 Kb
  • Biological Unit Coordinates (4um9.pdb2.gz) 309 Kb
  • LPC: Ligand-Protein Contacts for 4UM9
  • CSU: Contacts of Structural Units for 4UM9
  • Structure Factors (896 Kb)
  • Retrieve 4UM9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4UM9 from S2C, [Save to disk]
  • Re-refined 4um9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4UM9 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 4UM9
  • 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 4UM9, from MSDmotif at EBI
  • Fold representative 4um9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4um9_F] [4um9_C] [4um9] [4um9_D] [4um9_A] [4um9_E] [4um9_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4UM9: [EGF_like] [INB] [Int_alpha] [PSI] [VWA ] by SMART
  • Other resources with information on 4UM9
  • Community annotation for 4UM9 at PDBWiki (http://pdbwiki.org)

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