Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 187.43 kDa 
• Atom Count: 11700 
• Residue Count: 1471 
• Unique protein chains: 3

1L5G

CRYSTAL STRUCTURE OF THE EXTRACELLULAR SEGMENT OF INTEGRIN AVB3 IN COMPLEX WITH AN ARG-GLY-ASP LIGAND

• DOI: 10.2210/pdb1L5G/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2002-03-06 Released: 2002-04-17 
• Deposition Author(s): Xiong, J.-P., Stehle, T., Zhang, R., Joachimiak, A., Frech, M., Goodman, S.L., Arnaout, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.328 
• R-Value Work: 0.248 

Literature

Crystal structure of the extracellular segment of integrin alpha Vbeta3 in complex with an Arg-Gly-Asp ligand.

Xiong, J.P., Stehle, T., Zhang, R., Joachimiak, A., Frech, M., Goodman, S.L., Arnaout, M.A.

(2002) Science 296: 151-155

• PubMed: 11884718 
• DOI: 10.1126/science.1069040
• Primary Citation of Related Structures:  
  1M1X, 1L5G


• PubMed Abstract: 
  

The structural basis for the divalent cation-dependent binding of heterodimeric alphabeta integrins to their ligands, which contain the prototypical Arg-Gly-Asp sequence, is unknown. Interaction with ligands triggers tertiary and quaternary structural rearrangements in integrins that are needed for cell signaling. Here we report the crystal structure of the extracellular segment of integrin alphaVbeta3 in complex with a cyclic peptide presenting the Arg-Gly-Asp sequence. The ligand binds at the major interface between the alphaV and beta3 subunits and makes extensive contacts with both. Both tertiary and quaternary changes are observed in the presence of ligand. The tertiary rearrangements take place in betaA, the ligand-binding domain of beta3; in the complex, betaA acquires two cations, one of which contacts the ligand Asp directly and the other stabilizes the ligand-binding surface. Ligand binding induces small changes in the orientation of alphaV relative to beta3.

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Organizational Affiliation: 

Renal Unit, Leukocyte Biology and Inflammation Program, Structural Biology Program, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INTEGRIN ALPHA V	A	957	Homo sapiens	Mutation(s): 0  Gene Names: ITGAV, MSK8, VNRA, VTNR
Find proteins for P06756 (Homo sapiens) Explore P06756  Go to UniProtKB:  P06756
NIH Common Fund Data Resources
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
Find proteins for P05106 (Homo sapiens) Explore P05106  Go to UniProtKB:  P05106
NIH Common Fund Data Resources
PHAROS:  P05106 GTEx:  ENSG00000259207

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLIC ARG-GLY-ASP PEPTIDE	C	5	N/A	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E, F, H	2		N-Glycosylation

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, I, J	2		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MN	A, B	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MVA	C	L-PEPTIDE LINKING	C6 H13 N O2		VAL

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.328 
• R-Value Work: 0.248 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.79	α = 90
b = 129.79	β = 90
c = 308.78	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-03-06 
• Released Date: 2002-04-17 
Deposition Author(s): Xiong, J.-P., Stehle, T., Zhang, R., Joachimiak, A., Frech, M., Goodman, S.L., Arnaout, M.A.

Revision History 

• Version 1.0: 2002-04-17
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary