Macromolecule Content

• Total Structure Weight: 9.76 
• Atom Count: 1367 
• Residue Count: 86 
• Unique protein chains: 1

1G4F

NMR STRUCTURE OF THE FIFTH DOMAIN OF HUMAN BETA2-GLYCOPROTEIN I

• DOI: 10.2210/pdb1G4F/pdb
• BMRB: 4981

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2000-10-27 Released: 2000-11-15 
• Deposition Author(s): Hoshino, M., Hagihara, Y., Nishii, I., Yamazaki, T., Kato, H., Goto, Y.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Literature

Identification of the phospholipid-binding site of human beta(2)-glycoprotein I domain V by heteronuclear magnetic resonance.

Hoshino, M., Hagihara, Y., Nishii, I., Yamazaki, T., Kato, H., Goto, Y.

(2000) J Mol Biol 304: 927-939

• PubMed: 11124037 
• DOI: 10.1006/jmbi.2000.4243
• Structures With Same Primary Citation


• PubMed Abstract: 
  

To understand the mechanism of the interaction between human beta(2)-glycoprotein I (beta(2)-GPI) and negatively charged phospholipids, we determined the three-dimensional solution structure of the fifth domain of beta(2)-GPI by heteronuclear multidimensional NMR. The results showed that the molecule is composed of well-defined four anti-parallel beta-strands and two short alpha-helices, as well as a long highly flexible loop. Backbone dynamic analysis demonstrated significant mobility of the flexible loop on a subnanosecond time scale. Structural modeling of the nicked fifth domain, in which the Lys317-Thr318 peptide bond was specifically cleaved, revealed the importance of this long C-terminal loop for the interaction between beta(2)-GPI and negatively charged phospholipids. A titration experiment with the anionic surfactant SDS showed that this highly mobile loop, as well as the short beta-hairpin between betaC and betaD strands, which is rich in positively charged residues, specifically interact with the surfactant. The mobile loop, together with the surrounding positively charged residues, probably construct the binding site for negatively charged phospholipids such as cardiolipin.

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Organizational Affiliation: 

Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, 565-0871, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
BETA2-GLYCOPROTEIN I	A	86	Homo sapiens	Mutation(s): 1  Gene Names: APOH, B2G1
Find proteins for P02749 (Homo sapiens) Go to UniProtKB:  P02749
NIH Common Fund Data Resources
PHAROS  P02749 GTEx  ENSG00000091583

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 
• OLDERADO: 1G4F Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-10-27 
• Released Date: 2000-11-15 
Deposition Author(s): Hoshino, M., Hagihara, Y., Nishii, I., Yamazaki, T., Kato, H., Goto, Y.

Revision History 

• Version 1.0: 2000-11-15
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance