4UM9

Crystal structure of alpha V beta 6 with peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 

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This is version 2.0 of the entry. See complete history


Literature

Structural Determinants of Integrin Beta-Subunit Specificity for Latent Tgf-Beta

Dong, X.Hudson, N.E.Lu, C.Springer, T.A.

(2014) Nat Struct Mol Biol 21: 1091

  • DOI: 10.1038/nsmb.2905
  • Primary Citation of Related Structures:  
    4UM8, 4UM9

  • PubMed 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 ...

    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.


    Organizational Affiliation

    1] Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA. [2] Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
INTEGRIN ALPHA-VA, C604Homo sapiensMutation(s): 1 
Gene Names: ITGAVMSK8VNRAVTNR
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PHAROS:  P06756
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UniProt GroupP06756
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
INTEGRIN BETA-6B483Homo sapiensMutation(s): 0 
Gene Names: ITGB6
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PHAROS:  P18564
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
INTEGRIN BETA-6D483Homo sapiensMutation(s): 0 
Gene Names: ITGB6
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PHAROS:  P18564
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UniProt GroupP18564
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSFORMING GROWTH FACTOR BETA 3E, F13Homo sapiensMutation(s): 0 
Gene Names: TGFB3
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PHAROS:  P10600
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Oligosaccharides

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Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, J, K, L, M, P
G, J, K, L, M, P
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseH 4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22573RC
GlyCosmos:  G22573RC
GlyGen:  G22573RC
Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI, N 6N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G09724ZC
GlyCosmos:  G09724ZC
GlyGen:  G09724ZC
Entity ID: 8
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseO 3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
BA [auth B],
CA [auth B],
DA [auth B],
KA [auth C],
MA [auth C],
BA [auth B],
CA [auth B],
DA [auth B],
KA [auth C],
MA [auth C],
QA [auth D],
RA [auth D],
SA [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MAN
Query on MAN

Download Ideal Coordinates CCD File 
LA [auth C]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
SO4
Query on SO4

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EA [auth C],
FA [auth C],
Q [auth A],
R [auth A],
S [auth A],
EA [auth C],
FA [auth C],
Q [auth A],
R [auth A],
S [auth A],
X [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth B],
GA [auth C],
HA [auth C],
IA [auth C],
JA [auth C],
AA [auth B],
GA [auth C],
HA [auth C],
IA [auth C],
JA [auth C],
OA [auth D],
PA [auth D],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
Z [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
NA [auth D],
Y [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.02α = 90
b = 168.09β = 98.95
c = 101.8γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-12
    Type: Initial release
  • Version 1.1: 2014-11-19
    Changes: Database references
  • Version 1.2: 2014-12-17
    Changes: Database references
  • Version 1.3: 2016-03-16
    Changes: Database references, Derived calculations, Other, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary