Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36986.05 
• Atom Count: 2575 
• Residue Count: 319 
• Unique protein chains: 1

1QUB

CRYSTAL STRUCTURE OF THE GLYCOSYLATED FIVE-DOMAIN HUMAN BETA2-GLYCOPROTEIN I PURIFIED FROM BLOOD PLASMA

• DOI: 10.2210/pdb1QUB/pdb

• Classification: MEMBRANE ADHESION
• Organism(s): Homo sapiens


• Deposited: 1999-07-01 Released: 1999-10-08 
• Deposition Author(s): Bouma, B., de Groot, P.G., van den Elsen, J.M.H., Ravelli, R.B.G., Schouten, A., Simmelink, M.J.A., Derksen, R.H.W.M., Kroon, J., Gros, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.269 
• R-Value Work: 0.249 

Literature

Adhesion mechanism of human beta(2)-glycoprotein I to phospholipids based on its crystal structure.

Bouma, B., de Groot, P.G., van den Elsen, J.M., Ravelli, R.B., Schouten, A., Simmelink, M.J., Derksen, R.H., Kroon, J., Gros, P.

(1999) EMBO J. 18: 5166-5174

• PubMed: 10508150 
• DOI: 10.1093/emboj/18.19.5166


• PubMed Abstract: 
  

Human beta(2)-glycoprotein I is a heavily glycosylated five-domain plasma membrane-adhesion protein, which has been implicated in blood coagulation and clearance of apoptotic bodies from the circulation. It is also the key antigen in the autoimmune disease anti-phospholipid syndrome. The crystal structure of beta(2)-glycoprotein I isolated from human plasma reveals an elongated fish-hook-like arrangement of the globular short consensus repeat domains. Half of the C-terminal fifth domain deviates strongly from the standard fold, as observed in domains one to four. This aberrant half forms a specific phospholipid-binding site. A large patch of 14 positively charged residues provides electrostatic interactions with anionic phospholipid headgroups and an exposed membrane-insertion loop yields specificity for lipid layers. The observed spatial arrangement of the five domains suggests a functional partitioning of protein adhesion and membrane adhesion over the N- and C-terminal domains, respectively, separated by glycosylated bridging domains. Coordinates are in the Protein Data Bank (accession No. 1QUB).

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Organizational Affiliation: 

Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (human beta2-Glycoprotein I)	A	319	Homo sapiens	Mutation(s): 0  Gene Names: APOH (B2G1)
Find proteins for P02749 (Homo sapiens) Go to Gene View: APOH Go to UniProtKB:  P02749

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MAN	A	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.269 
• R-Value Work: 0.249 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 161.170	α = 90.00
b = 166.490	β = 90.00
c = 114.510	γ = 90.00

Software Package:

Software Name	Purpose
TRUNCATE	data reduction
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-07-01 
• Released Date: 1999-10-08 
• Deposition Author(s): Bouma, B., de Groot, P.G., van den Elsen, J.M.H., Ravelli, R.B.G., Schouten, A., Simmelink, M.J.A., Derksen, R.H.W.M., Kroon, J., Gros, P.

Revision History 

• Version 1.0: 1999-10-08
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance
• Version 1.3: 2018-01-24
  Type: Structure summary