3OP8

Crystal structure of the domain V from beta2-glycoprotein I

• PDB DOI: https://doi.org/10.2210/pdb3OP8/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2010-08-31 Released: 2011-01-05 
• Deposition Author(s): Kolyada, A., Lee, C.-J., De Biasio, A., Beglova, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.219 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Literature

A Novel Dimeric Inhibitor Targeting Beta2GPI in Beta2GPI/Antibody Complexes Implicated in Antiphospholipid Syndrome.

Kolyada, A., Lee, C.J., De Biasio, A., Beglova, N.

(2010) PLoS One 5: e15345-e15345

• PubMed: 21179511 
• DOI: https://doi.org/10.1371/journal.pone.0015345
• Primary Citation of Related Structures:  
  3OP8


• PubMed Abstract: 
  

  β2GPI is a major antigen for autoantibodies associated with antiphospholipid syndrome (APS), an autoimmune disease characterized by thrombosis and recurrent pregnancy loss. Only the dimeric form of β2GPI generated by anti-β2GPI antibodies is pathologically important, in contrast to monomeric β2GPI which is abundant in plasma.

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Organizational Affiliation: 

Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, United States of America.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19.55 kDa 
• Atom Count: 1,469 
• Modelled Residue Count: 170 
• Deposited Residue Count: 170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-glycoprotein 1	A, B	85	Homo sapiens	Mutation(s): 0  Gene Names: APOH, B2GPI Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P02749 (Homo sapiens) Explore P02749  Go to UniProtKB:  P02749
PHAROS:  P02749 GTEx:  ENSG00000091583

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.219 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.29	α = 93.83
b = 38.09	β = 102.65
c = 49.51	γ = 90.09

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-05 
Deposition Author(s): Kolyada, A., Lee, C.-J., De Biasio, A., Beglova, N.

Revision History  

• Version 1.0: 2011-01-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance