Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 186.85 kDa 
• Atom Count: 12115 
• Modelled Residue Count: 1526 
• Deposited 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
• Mutation(s): No 


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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.367 
• R-Value Work: 0.293 
• R-Value Observed: 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
• Primary Citation of Related Structures:  
  1U8C


• 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.

---

Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-V	A	957	Homo sapiens	Mutation(s): 0  Gene Names: ITGAV, VNRA, MSK8, 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

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E, G	2		N-Glycosylation

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	J [auth A], K [auth A], L [auth A], R [auth B], S [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], T [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.367 
• R-Value Work: 0.293 
• R-Value Observed: 0.293 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130	α = 90
b = 130	β = 90
c = 307.3	γ = 120

Software Package:

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

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
  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