4MMY

Integrin AlphaVBeta3 ectodomain bound to the tenth domain of Fibronectin with the IAKGDWND motif


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.183 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for pure antagonism of integrin alpha V beta 3 by a high-affinity form of fibronectin.

Van Agthoven, J.F.Xiong, J.P.Alonso, J.L.Rui, X.Adair, B.D.Goodman, S.L.Arnaout, M.A.

(2014) Nat.Struct.Mol.Biol. 21: 383-388

  • DOI: 10.1038/nsmb.2797
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Integrins are important therapeutic targets. However, current RGD-based anti-integrin drugs are also partial agonists, inducing conformational changes that trigger potentially fatal immune reactions and paradoxical cell adhesion. Here we describe the ...

    Integrins are important therapeutic targets. However, current RGD-based anti-integrin drugs are also partial agonists, inducing conformational changes that trigger potentially fatal immune reactions and paradoxical cell adhesion. Here we describe the first crystal structure of αVβ3 bound to a physiologic ligand, the tenth type III RGD domain of wild-type fibronectin (wtFN10), or to a high-affinity mutant (hFN10) shown here to act as a pure antagonist. Comparison of these structures revealed a central π-π interaction between Trp1496 in the RGD-containing loop of hFN10 and Tyr122 of the β3 subunit that blocked conformational changes triggered by wtFN10 and trapped hFN10-bound αVβ3 in an inactive conformation. Removing the Trp1496 or Tyr122 side chains or reorienting Trp1496 away from Tyr122 converted hFN10 into a partial agonist. These findings offer new insights into the mechanism of integrin activation and a basis for the design of RGD-based pure antagonists.


    Organizational Affiliation

    1] Structural Biology Program, Department of Medicine, Harvard Medical School, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [2].




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrin alpha-V
A
959Homo sapiensMutation(s): 0 
Gene Names: ITGAV (MSK8, VNRA, VTNR)
Find proteins for P06756 (Homo sapiens)
Go to Gene View: ITGAV
Go to UniProtKB:  P06756
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Integrin beta-3
B
692Homo sapiensMutation(s): 0 
Gene Names: ITGB3 (GP3A)
Find proteins for P05106 (Homo sapiens)
Go to Gene View: ITGB3
Go to UniProtKB:  P05106
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fibronectin
C
98Homo sapiensMutation(s): 6 
Gene Names: FN1 (FN)
Find proteins for P02751 (Homo sapiens)
Go to Gene View: FN1
Go to UniProtKB:  P02751
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.183 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.211 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 130.018α = 90.00
b = 130.018β = 90.00
c = 308.203γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
DENZOdata reduction
PHASERphasing
PHENIXrefinement
HKL-2000data scaling
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-26
    Type: Initial release
  • Version 1.1: 2014-04-09
    Type: Database references
  • Version 1.2: 2014-04-30
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description