2FYL

Haddock model of the complex between double module of LRP, CR56, and first domain of receptor associated protein, RAP-d1.


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 
  • Selection Criteria: Best averaged HADDOCK score 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Binding Site Structure of One LRP-RAP Complex:Implications for a Common Ligand-Receptor Binding Motif.

Jensen, G.A.Andersen, O.M.Bonvin, A.M.Bjerrum-Bohr, I.Etzerodt, M.O'shea, C.Poulsen, F.M.Kragelund, B.B.

(2006) J Mol Biol 362: 700-716

  • DOI: 10.1016/j.jmb.2006.07.013
  • Primary Citation of Related Structures:  
    2FYL, 2FYJ

  • PubMed Abstract: 
  • The low-density lipoprotein receptor-related protein (LRP) interacts with more than 30 ligands of different sizes and structures that can all be replaced by the receptor-associated protein (RAP). The double module of complement type repeats, CR56, of LRP binds many ligands including all three domains of RAP and alpha2-macroglobulin, which promotes the catabolism of the Abeta-peptide implicated in Alzheimer's disease ...

    The low-density lipoprotein receptor-related protein (LRP) interacts with more than 30 ligands of different sizes and structures that can all be replaced by the receptor-associated protein (RAP). The double module of complement type repeats, CR56, of LRP binds many ligands including all three domains of RAP and alpha2-macroglobulin, which promotes the catabolism of the Abeta-peptide implicated in Alzheimer's disease. To understand the receptor-ligand cross-talk, the NMR structure of CR56 has been solved and ligand binding experiments with RAP domain 1 (RAPd1) have been performed. From chemical shift perturbations of both binding partners upon complex formation, a HADDOCK model of the complex between CR56 and RAPd1 has been obtained. The binding residues are similar to a common binding motif suggested from alpha2-macroglobulin binding studies and provide evidence for an understanding of their mutual cross-competition pattern. The present structural results convey a simultaneous description of both binding partners of an LRP-ligand complex and open a route to a broader understanding of the binding specificity of the LRP receptor, which may involve a general four-residue receptor-ligand recognition motif common to all LRP ligands. The present result may be beneficial in the design of antagonists of ligand binding to the LDL receptor family, and especially of drugs for treatment of Alzheimer's disease.


    Organizational Affiliation

    SBiN Lab, Institute of Molecular Biology and Physiology, University of Copenhagen, Ă˜ster Farimagsgade 2A, DK-1353 Copenhagen K, Denmark.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-2-macroglobulin receptor-associated protein A81Homo sapiensMutation(s): 0 
Gene Names: LRPAP1A2MRAP
Find proteins for P30533 (Homo sapiens)
Explore P30533 
Go to UniProtKB:  P30533
NIH Common Fund Data Resources
PHAROS:  P30533
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Low-density lipoprotein receptor-related protein 1 B82Homo sapiensMutation(s): 0 
Gene Names: LRP1A2MRAPR
Find proteins for Q07954 (Homo sapiens)
Explore Q07954 
Go to UniProtKB:  Q07954
NIH Common Fund Data Resources
PHAROS:  Q07954
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 
  • Selection Criteria: Best averaged HADDOCK score 
  • OLDERADO: 2FYL Olderado

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-10
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance