Biological Assembly 1  

 3D View: Structure | 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: 186973.89 
• Atom Count: 12115 
• Residue Count: 1649 
• Unique protein chains: 2

1U8C

A novel adaptation of the integrin PSI domain revealed from its crystal structure

• DOI: 10.2210/pdb1U8C/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda


• Deposited: 2004-08-05 Released: 2004-12-28 
• Deposition Author(s): Xiong, J.P., Stehle, T., Goodman, S.L., Arnaout, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.1 Å
• R-Value Free: 0.367 
• R-Value Work: 0.293 

Literature

A novel adaptation of the integrin PSI domain revealed from its crystal structure.

Xiong, J.P., Stehle, T., Goodman, S.L., Arnaout, M.A.

(2004) J.Biol.Chem. 279: 40252-40254

• PubMed: 15299032 
• DOI: 10.1074/jbc.C400362200


• PubMed Abstract: 
  

Integrin beta-subunits contain an N-terminal PSI (for plexin-semaphorin-integrin) domain that contributes to integrin activation and harbors the PI(A) alloantigen associated with immune thrombocytopenias and susceptibility to sudden cardiac death. Here we report the crystal structure of PSI in the context of the crystallized alphaVbeta3 ectodomain. The integrin PSI forms a two-stranded antiparallel beta-sheet flanked by two short helices; its long interstrand loop houses Pl(A) and may face the EGF2 domain. The integrin PSI contains four cysteine pairs connected in a 1-4, 2-8, 3-6, 5-7 pattern. An unexpected feature of the structure is that the final, eighth cysteine is located C-terminal to the Ig-like hybrid domain and is thus separated by the hybrid domain from the other seven cysteines of PSI. This architecture may be relevant to the evolution of integrins and should help refine the current models of integrin activation.

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Organizational Affiliation: 

Structural Biology Program, Leukocyte Biology and Inflammation Program, Renal Unit.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Integrin alpha-V	A	957	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CA	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NDG	A, B	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-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: 3.1 Å
• R-Value Free: 0.367 
• R-Value Work: 0.293 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 130.000	α = 90.00
b = 130.000	β = 90.00
c = 307.300	γ = 120.00

Software Package:

Software Name	Purpose
CNS	phasing
SCALEPACK	data scaling
CNS	refinement
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-08-05 
• Released Date: 2004-12-28 
• Deposition Author(s): Xiong, J.P., Stehle, T., Goodman, S.L., Arnaout, M.A.

Revision History 

• Version 1.0: 2004-12-28
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance