Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - ABCD Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer -A2BC 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 236405.23 
• Atom Count: 13526 
• Residue Count: 2086 
• Unique protein chains: 4

4O02

AlphaVBeta3 integrin in complex with monoclonal antibody FAB fragment.

• DOI: 10.2210/pdb4O02/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda


• Deposited: 2013-12-13 Released: 2014-04-02 
• Deposition Author(s): Mahalingam, B., van Agthoven, J., Xiong, J., Arnaout, M.A.

---

Experimental Data Snapshot

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

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

• PubMed: 24692540 
• 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 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
Molecule	Chains	Sequence Length	Organism	Details
Integrin alpha-V	A	962	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Integrin beta-3	B	692	Homo sapiens	Mutation(s): 0  Gene Names: ITGB3 (GP3A)
Find proteins for P05106 (Homo sapiens) Go to Gene View: ITGB3 Go to UniProtKB:  P05106

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
17E6 light chain	L	214	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
17E6 heavy chain	H	218	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MN	A, B	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
MAN	A	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA	A	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NO3	A	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
NAG	A, B	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

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 = 110.464	α = 90.00
b = 266.988	β = 90.00
c = 102.163	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
PHASER	phasing
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-12-13 
• Released Date: 2014-04-02 
• Deposition Author(s): Mahalingam, B., van Agthoven, J., Xiong, J., Arnaout, M.A.

Revision History 

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