Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 236.04 kDa 
• Atom Count: 13526 
• Modelled Residue Count: 2034 
• Deposited Residue Count: 2086 
• Unique protein chains: 4

4O02

AlphaVBeta3 integrin in complex with monoclonal antibody FAB fragment.

• PDB DOI: 10.2210/pdb4O02/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 0.312 
• R-Value Work: 0.246 
• R-Value Observed: 0.250 

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
• Primary Citation of Related Structures:  
  4O02


• 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.

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Organizational Affiliation: 

From the Structural Biology Program and the Leukocyte Biology and Inflammation Program, Departments of Medicine and Developmental & Regenerative Biology, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts 02129, [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-V	A	962	Homo sapiens	Mutation(s): 0  Gene Names: ITGAV, MSK8, VNRA, VTNR
UniProt & NIH Common Fund Data Resources
Find proteins for P06756 (Homo sapiens) Explore P06756  Go to UniProtKB:  P06756
PHAROS:  P06756 GTEx:  ENSG00000138448

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin beta-3	B	692	Homo sapiens	Mutation(s): 0  Gene Names: ITGB3, GP3A
UniProt & NIH Common Fund Data Resources
Find proteins for P05106 (Homo sapiens) Explore P05106  Go to UniProtKB:  P05106
PHAROS:  P05106 GTEx:  ENSG00000259207

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
17E6 light chain	C [auth L]	214	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
17E6 heavy chain	D [auth H]	218	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-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-glucopyranose	E [auth C]	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G31387PS GlyCosmos:  G31387PS GlyGen:  G31387PS

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth D]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 7
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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-glucopyranose	G [auth E]	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G09724ZC GlyCosmos:  G09724ZC GlyGen:  G09724ZC

Entity ID: 8
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth F], J [auth I], K [auth J]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 9
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-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-glucopyranose	I [auth G]	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G06726TJ GlyCosmos:  G06726TJ GlyGen:  G06726TJ

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	L [auth A], S [auth B], T [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NO3	Q [auth A], R [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
MN	M [auth A], N [auth A], O [auth A], P [auth A], U [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 0.312 
• R-Value Work: 0.246 
• R-Value Observed: 0.250 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.464	α = 90
b = 266.988	β = 90
c = 102.163	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
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
  Changes: Database references, Derived calculations
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary