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PDBsum entry 4um8

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protein ligands metals Protein-protein interface(s) links
Immune system PDB id
4um8

 

 

 

 

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Contents
Protein chains
591 a.a.
423 a.a.
Ligands
NAG-NAG-BMA-MAN ×3
NAG-NAG-BMA-MAN-
MAN
×2
NAG-NAG-BMA-MAN-
MAN-MAN
×2
NAG-NAG-BMA ×2
NAG-NAG ×3
NAG-NAG-BMA-MAN-
MAN-MAN-MAN
SO4 ×3
CAC ×2
NAG ×3
Metals
_CA ×10
_CL ×3
_NI
_MG ×2
Waters ×161
PDB id:
4um8
Name: Immune system
Title: Crystal structure of alpha v beta 6
Structure: Integrin alpha-v. Chain: a, c. Fragment: headpiece, residues 31-625. Synonym: vitronectin receptor subunit alpha, integrin alpha v. Engineered: yes. Mutation: yes. Integrin beta-6. Chain: b, d. Synonym: integrin beta 6.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: hek293s gnt i- cell.
Resolution:
2.85Å     R-factor:   0.240     R-free:   0.281
Authors: X.Dong,T.A.Springer
Key ref: X.Dong et al. (2014). Structural determinants of integrin β-subunit specificity for latent TGF-β. Nat Struct Biol, 21, 1091-1096. PubMed id: 25383667 DOI: 10.1038/nsmb.2905
Date:
15-May-14     Release date:   12-Nov-14    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P06756  (ITAV_HUMAN) -  Integrin alpha-V from Homo sapiens
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1048 a.a.
591 a.a.*
Protein chains
Pfam   ArchSchema ?
P18564  (ITB6_HUMAN) -  Integrin beta-6 from Homo sapiens
Seq:
Struc:
 
Seq:
Struc:
788 a.a.
423 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 

 
DOI no: 10.1038/nsmb.2905 Nat Struct Biol 21:1091-1096 (2014)
PubMed id: 25383667  
 
 
Structural determinants of integrin β-subunit specificity for latent TGF-β.
X.Dong, N.E.Hudson, C.Lu, T.A.Springer.
 
  ABSTRACT  
 
Eight integrin α-β heterodimers recognize ligands with an Arg-Gly-Asp (RGD) motif. However, the structural mechanism by which integrins differentiate among extracellular proteins with RGD motifs is not understood. Here, crystal structures, mutations and peptide-affinity measurements show that αVβ6 binds with high affinity to a RGDLXXL/I motif within the prodomains of TGF-β1 and TGF-β3. The LXXL/I motif forms an amphipathic α-helix that binds in a hydrophobic pocket in the β6 subunit. Elucidation of the basis for ligand binding specificity by the integrin β subunit reveals contributions by three different βI-domain loops, which we designate specificity-determining loops (SDLs) 1, 2 and 3. Variation in a pair of single key residues in SDL1 and SDL3 correlates with the variation of the entire β subunit in integrin evolution, thus suggesting a paradigmatic role in overall β-subunit function.
 

 

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