4O02

AlphaVBeta3 integrin in complex with monoclonal antibody FAB fragment.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.605 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Atomic basis for the species-specific inhibition of alpha V integrins by monoclonal antibody 17E6 is revealed by the crystal structure of alpha V beta 3 ectodomain-17E6 Fab complex.

Mahalingam, B.Van Agthoven, J.F.Xiong, J.P.Alonso, J.L.Adair, B.D.Rui, X.Anand, S.Mehrbod, M.Mofrad, M.R.Burger, C.Goodman, S.L.Arnaout, M.A.

(2014) J.Biol.Chem. 289: 13801-13809

  • DOI: 10.1074/jbc.M113.546929

  • PubMed Abstract: 
  • The function-blocking, non-RGD-containing, and primate-specific mouse monoclonal antibody 17E6 binds the αV subfamily of integrins. 17E6 is currently in phase II clinical trials for treating cancer. To elucidate the structural basis of recognition an ...

    The function-blocking, non-RGD-containing, and primate-specific mouse monoclonal antibody 17E6 binds the αV subfamily of integrins. 17E6 is currently in phase II clinical trials for treating cancer. To elucidate the structural basis of recognition and the molecular mechanism of inhibition, we crystallized αVβ3 ectodomain in complex with the Fab fragment of 17E6. Protein crystals grew in presence of the activating cation Mn(2+). The integrin in the complex and in solution assumed the genuflected conformation. 17E6 Fab bound exclusively to the Propeller domain of the αV subunit. At the core of αV-Fab interface were interactions involving Propeller residues Lys-203 and Gln-145, with the latter accounting for primate specificity. The Propeller residue Asp-150, which normally coordinates Arg of the ligand Arg-Gly-Asp motif, formed contacts with Arg-54 of the Fab that were expected to reduce soluble FN10 binding to cellular αVβ3 complexed with 17E6. This was confirmed in direct binding studies, suggesting that 17E6 is an allosteric inhibitor of αV integrins.


    Organizational Affiliation

    From the Structural Biology Program and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrin alpha-V
A
962Homo 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
17E6 light chain
L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
17E6 heavy chain
H
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 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
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NO3
Query on NO3

Download SDF File 
Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-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: 3.605 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.246 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 110.464α = 90.00
b = 266.988β = 90.00
c = 102.163γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2015-02-25
    Type: Database references, Derived calculations