1QUB

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • 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 d ...

    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).


    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
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (human beta2-Glycoprotein I)
A
319Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
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 = 161.170α = 90.00
b = 166.490β = 90.00
c = 114.510γ = 90.00
Software Package:
Software NamePurpose
TRUNCATEdata reduction
MOSFLMdata reduction
CCP4data scaling
SOLVEphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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