2KRI

Structure of a complex between domain V of beta2-glycoprotein I and the fourth ligand-binding module from LDLR determined with Haddock


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 
  • Selection Criteria: lowest haddock score 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mode of interaction between beta2GPI and lipoprotein receptors suggests mutually exclusive binding of beta2GPI to the receptors and anionic phospholipids.

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

(2010) Structure 18: 366-376

  • DOI: https://doi.org/10.1016/j.str.2009.12.013
  • Primary Citation of Related Structures:  
    2KRI

  • PubMed Abstract: 

    Lipoprotein receptors of the LDLR family serve as clearance receptors for beta2GPI and as signaling receptors for the beta2GPI/antibody complexes in antiphospholipid syndrome. We compared four ligand-binding LA modules from LDLR and ApoER2 for their ability to bind domain V of beta2GPI (beta2GPI-DV). We found that the LA modules capable of binding beta2GPI-DV interact with the same region on beta2GPI-DV using residues at their calcium-coordination site. The structure of a complex between beta2GPI-DV and LA4 of LDLR, solved by molecular docking guided by NMR-derived restraints and extensively validated, represents the general mode of interaction between beta2GPI and lipoprotein receptors. We have shown that beta2GPI-DV cannot simultaneously bind to lipoprotein receptors and anionic phospholipids, suggesting that the association of beta2GPI/anti-beta2GPI antibody complexes with anionic phospholipids will interfere with lipoprotein receptors' signaling in APS.


  • Organizational Affiliation

    Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-glycoprotein 185Homo sapiensMutation(s): 0 
Gene Names: APOHB2G1
UniProt & NIH Common Fund Data Resources
Find proteins for P02749 (Homo sapiens)
Explore P02749 
Go to UniProtKB:  P02749
PHAROS:  P02749
GTEx:  ENSG00000091583 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02749
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Low-density lipoprotein receptor40Homo sapiensMutation(s): 0 
Gene Names: LDLR
UniProt & NIH Common Fund Data Resources
Find proteins for P01130 (Homo sapiens)
Explore P01130 
Go to UniProtKB:  P01130
PHAROS:  P01130
GTEx:  ENSG00000130164 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01130
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 
  • Selection Criteria: lowest haddock score 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2010-03-31 
  • Deposition Author(s): Beglova, N.

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-11-06
    Changes: Data collection, Database references, Derived calculations, Experimental preparation