Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 191211.20 
• Atom Count: 13087 
• Residue Count: 1662 
• Unique protein chains: 2

3IJE

Crystal structure of the complete integrin alhaVbeta3 ectodomain plus an Alpha/beta transmembrane fragment

• DOI: 10.2210/pdb3IJE/pdb

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


• Deposited: 2009-08-04 Released: 2009-09-29 
• Deposition Author(s): Xiong, J.-P., Mahalingham, B., Rui, X., Hyman, B.T., Goodman, S.L., Arnaout, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.285 
• R-Value Work: 0.244 

Literature

Crystal structure of the complete integrin alphaVbeta3 ectodomain plus an alpha/beta transmembrane fragment.

Xiong, J.P., Mahalingham, B., Alonso, J.L., Borrelli, L.A., Rui, X., Anand, S., Hyman, B.T., Rysiok, T., Muller-Pompalla, D., Goodman, S.L., Arnaout, M.A.

(2009) J.Cell Biol. 186: 589-600

• PubMed: 19704023 
• DOI: 10.1083/jcb.200905085
• Also Cited By: 4G1M


• PubMed Abstract: 
  

We determined the crystal structure of 1TM-alphaVbeta3, which represents the complete unconstrained ectodomain plus short C-terminal transmembrane stretches of the alphaV and beta3 subunits. 1TM-alphaVbeta3 is more compact and less active in solution when compared with DeltaTM-alphaVbeta3, which lacks the short C-terminal stretches. The structure reveals a bent conformation and defines the alpha-beta interface between IE2 (EGF-like 2) and the thigh domains. Modifying this interface by site-directed mutagenesis leads to robust integrin activation. Fluorescent lifetime imaging microscopy of inactive full-length alphaVbeta3 on live cells yields a donor-membrane acceptor distance, which is consistent with the bent conformation and does not change in the activated integrin. These data are the first direct demonstration of conformational coupling of the integrin leg and head domains, identify the IE2-thigh interface as a critical steric barrier in integrin activation, and suggest that inside-out activation in intact cells may involve conformational changes other than the postulated switch to a genu-linear state.

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Organizational Affiliation: 

Program in Leukocyte Biology and Inflammation, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Integrin alpha-V	A	967	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	695	Homo sapiens	Mutation(s): 0  Gene Names: ITGB3 (GP3A)
Find proteins for P05106 (Homo sapiens) Go to Gene View: ITGB3 Go to UniProtKB:  P05106

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CA	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MAN	A	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA	A, B	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-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: 2.9 Å
• R-Value Free: 0.285 
• R-Value Work: 0.244 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 129.870	α = 90.00
b = 129.870	β = 90.00
c = 305.900	γ = 120.00

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
CNS	phasing
HKL-2000	data reduction
HKL-2000	data collection
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-08-04 
• Released Date: 2009-09-29 
• Deposition Author(s): Xiong, J.-P., Mahalingham, B., Rui, X., Hyman, B.T., Goodman, S.L., Arnaout, M.A.

Revision History 

• Version 1.0: 2009-09-29
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Advisory, Version format compliance
• Version 1.2: 2018-01-24
  Type: Advisory, Structure summary
• Version 1.3: 2019-07-24
  Type: Data collection, Derived calculations, Refinement description