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PDBsum entry 1yxk

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protein Protein-protein interface(s) links
Lipid binding protein PDB id
1yxk
Jmol
Contents
Protein chain
130 a.a. *
Waters ×52
* Residue conservation analysis
PDB id:
1yxk
Name: Lipid binding protein
Title: Crystal structure of human lectin-like oxidized low-density lipoprotein receptor 1 (lox-1) disulfide-linked dimer
Structure: Oxidised low density lipoprotein (lectin-like) receptor 1. Chain: a, b. Fragment: ligand-binding domain. Synonym: lox-1. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.40Å     R-factor:   0.218     R-free:   0.277
Authors: I.Ohki,T.Ishigaki,T.Oyama,S.Matsunaga,Q.Xie,M.Ohnishi- Kameyama,T.Murata,D.Tsuchiya,S.Machida,K.Morikawa,S.Tate
Key ref:
I.Ohki et al. (2005). Crystal structure of human lectin-like, oxidized low-density lipoprotein receptor 1 ligand binding domain and its ligand recognition mode to OxLDL. Structure, 13, 905-917. PubMed id: 15939022 DOI: 10.1016/j.str.2005.03.016
Date:
22-Feb-05     Release date:   14-Jun-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P78380  (OLR1_HUMAN) -  Oxidized low-density lipoprotein receptor 1
Seq:
Struc:
273 a.a.
130 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     carbohydrate binding     1 term  

 

 
DOI no: 10.1016/j.str.2005.03.016 Structure 13:905-917 (2005)
PubMed id: 15939022  
 
 
Crystal structure of human lectin-like, oxidized low-density lipoprotein receptor 1 ligand binding domain and its ligand recognition mode to OxLDL.
I.Ohki, T.Ishigaki, T.Oyama, S.Matsunaga, Q.Xie, M.Ohnishi-Kameyama, T.Murata, D.Tsuchiya, S.Machida, K.Morikawa, S.Tate.
 
  ABSTRACT  
 
Lectin-like, oxidized low-density lipoprotein (LDL) receptor 1, LOX-1, is the major receptor for oxidized LDL (OxLDL) in endothelial cells. We have determined the crystal structure of the ligand binding domain of LOX-1, with a short stalk region connecting the domain to the membrane-spanning region, as a homodimer linked by an interchain disulfide bond. In vivo assays with LOX-1 mutants revealed that the "basic spine," consisting of linearly aligned arginine residues spanning over the dimer surface, is responsible for ligand binding. Single amino acid substitution in the dimer interface caused a severe reduction in LOX-1 binding activity, suggesting that the correct dimer arrangement is crucial for binding to OxLDL. Based on the LDL model structure, possible binding modes of LOX-1 to OxLDL are proposed.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. The Empty Cavity in the Dimer Interface of LOX-1
(A) Empty cavity located at the dimer interface in the LOX-1 disulfide-lined dimer structure. The surrounding residues of the cavity are shown as bold lines.
(B) Possible effect of the W150A mutation on the basic spine structure on the LOX-1 ligand recognition surface. The W150A mutation may resize the empty cavity in the dimer interface, which subsequently disarranges the dimer, resulting in the disruption of the basic spine structure. The disrupted basic spine structure should lead to severe reduction of the binding ability to ligands.
(C) A plausible representation of the entire structure of LOX-1 at the cell surface, based on the crystal structure for CTLD and the model structure for the NECK. Modeling was performed by using the myosin heavy chain coiled-coil structure, which shows a high level of sequence homology to the NECK region.
(D) Scale comparison between the the OxLDL particle and LOX-1 dimer. The assembled structure of LOX-1 is drawn according to the results of cell biology studies that showed LOX-1 to exist as a hexamer on the cell surface (Xie et al., 2004). The diameter of OxLDL was estimated from cryoelectron microscopic observation of the LDL particle (Segrest et al., 2001). In this comparison, it is assumed that no significant structural alterations are induced by oxidation to the LDL particle.
 
  The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 905-917) copyright 2005.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19247493 S.Biocca, M.Falconi, I.Filesi, F.Baldini, L.Vecchione, R.Mango, F.Romeo, G.Federici, A.Desideri, and G.Novelli (2009).
Functional analysis and molecular dynamics simulation of LOX-1 K167N polymorphism reveal alteration of receptor activity.
  PLoS ONE, 4, e4648.  
  20073134 S.Iwamoto, N.Nishimichi, Y.Tateishi, Y.Sato, H.Horiuchi, S.Furusawa, T.Sawamura, and H.Matsuda (2009).
Generation and characterization of chicken monoclonal antibodies against human LOX-1.
  MAbs, 1, 357-363.  
19664054 W.Cao, V.Calabro, A.Root, G.Yan, K.Lam, S.Olland, J.Sanford, A.Robak, R.Zollner, Z.Lu, M.Ait-Zahra, R.Agostinelli, L.Tchistiakova, D.Gill, D.Harnish, J.Paulsen, and H.H.Shih (2009).
Oligomerization is required for the activity of recombinant soluble LOX-1.
  FEBS J, 276, 4909-4920.  
18597489 E.Hooley, E.Papagrigoriou, A.Navdaev, A.V.Pandey, J.M.Clemetson, K.J.Clemetson, and J.Emsley (2008).
The crystal structure of the platelet activator aggretin reveals a novel (alphabeta)2 dimeric structure.
  Biochemistry, 47, 7831-7837.
PDB code: 3bx4
18384690 J.W.Knowles, T.L.Assimes, E.Boerwinkle, S.P.Fortmann, A.Go, M.L.Grove, M.Hlatky, C.Iribarren, J.Li, R.Myers, N.Risch, S.Sidney, A.Southwick, K.A.Volcik, and T.Quertermous (2008).
Failure to replicate an association of SNPs in the oxidized LDL receptor gene (OLR1) with CAD.
  BMC Med Genet, 9, 23.  
18245080 N.S.Kar, M.Z.Ashraf, M.Valiyaveettil, and E.A.Podrez (2008).
Mapping and characterization of the binding site for specific oxidized phospholipids and oxidized low density lipoprotein of scavenger receptor CD36.
  J Biol Chem, 283, 8765-8771.  
17132623 A.A.Watson, J.Brown, K.Harlos, J.A.Eble, T.S.Walter, and C.A.O'Callaghan (2007).
The crystal structure and mutational binding analysis of the extracellular domain of the platelet-activating receptor CLEC-2.
  J Biol Chem, 282, 3165-3172.
PDB code: 2c6u
17988382 M.Falconi, S.Biocca, G.Novelli, and A.Desideri (2007).
Molecular dynamics simulation of human LOX-1 provides an explanation for the lack of OxLDL binding to the Trp150Ala mutant.
  BMC Struct Biol, 7, 73.  
17614937 X.P.Chen, T.T.Zhang, and G.H.Du (2007).
Lectin-like oxidized low-density lipoprotein receptor-1, a new promising target for the therapy of atherosclerosis?
  Cardiovasc Drug Rev, 25, 146-161.  
17125150 R.L.Rich, and D.G.Myszka (2006).
Survey of the year 2005 commercial optical biosensor literature.
  J Mol Recognit, 19, 478-534.  
16336259 A.N.Zelensky, and J.E.Gready (2005).
The C-type lectin-like domain superfamily.
  FEBS J, 272, 6179-6217.  
15939013 T.Sawamura (2005).
LOX-1 unlocked.
  Structure, 13, 834-835.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.