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PDBsum entry 1f5y
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protein metals links
Lipid binding protein PDB id
1f5y

 

 

 

 

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Contents
Protein chain
85 a.a. *
Metals
_CA ×2
* Residue conservation analysis
PDB id:
1f5y
Name: Lipid binding protein
Title: Nmr structure of a concatemer of the first and second ligand-binding modules of the human ldl receptor
Structure: Low-density lipoprotein receptor. Chain: a. Fragment: ligand-binding modules 1-2. Synonym: ldl receptor. Engineered: yes. Other_details: ligand-binding module concatemer
Source: Homo sapiens. Human. Organism_taxid: 9606. Organ: liver. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 20 models
Authors: N.D.Kurniawan,A.R.Atkins,I.M.Brereton,P.A.Kroon,R.Smith
Key ref: N.D.Kurniawan et al. (2000). NMR structure of a concatemer of the first and second ligand-binding modules of the human low-density lipoprotein receptor. Protein Sci, 9, 1282-1293. PubMed id: 10933493 DOI: 10.1110/ps.9.7.1282
Date:
18-Jun-00     Release date:   30-Aug-00    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P01130  (LDLR_HUMAN) -  Low-density lipoprotein receptor from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		860 a.a.
85 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 

 
DOI no: 10.1110/ps.9.7.1282 Protein Sci 9:1282-1293 (2000)
PubMed id: 10933493  
 
 
NMR structure of a concatemer of the first and second ligand-binding modules of the human low-density lipoprotein receptor.
N.D.Kurniawan, A.R.Atkins, S.Bieri, C.J.Brown, I.M.Brereton, P.A.Kroon, R.Smith.
 
  ABSTRACT  
 
The ligand-binding domain of the human low-density lipoprotein receptor consists of seven modules, each of 40-45 residues. In the presence of calcium, these modules adopt a common polypeptide fold with three conserved disulfide bonds. A concatemer of the first and second modules (LB(1-2)) folds efficiently in the presence of calcium ions, forming the same disulfide connectivities as in the isolated modules. The three-dimensional structure of LB(1-2) has now been solved using two-dimensional 1H NMR spectroscopy and restrained molecular dynamics calculations. No intermodule nuclear Overhauser effects were observed, indicating the absence of persistent interaction between them. The near random-coil NH and H alpha chemical shifts and the low phi and psi angle order parameters of the four-residue linker suggest that it has considerable flexibility. The family of LB(1-2) structures superimposed well over LB1 or LB2, but not over both modules simultaneously. LB1 and LB2 have a similar pattern of calcium ligands, but the orientations of the indole rings of the tryptophan residues W23 and W66 differ, with the latter limiting solvent access to the calcium ion. From these studies, it appears that although most of the modules in the ligand-binding region of the receptor are joined by short segments, these linkers may impart considerable flexibility on this region.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  18626063 A.P.Lillis, L.B.Van Duyn, J.E.Murphy-Ullrich, and D.K.Strickland (2008).
LDL receptor-related protein 1: unique tissue-specific functions revealed by selective gene knockout studies.
  Physiol Rev, 88, 887-918.  
18331356 S.D.Roosendaal, J.Kerver, M.Schipper, K.W.Rodenburg, and D.J.Van der Horst (2008).
The complex of the insect LDL receptor homolog, lipophorin receptor, LpR, and its lipoprotein ligand does not dissociate under endosomal conditions.
  FEBS J, 275, 1751-1766.  
15952897 H.Jeon, and S.C.Blacklow (2005).
Structure and physiologic function of the low-density lipoprotein receptor.
  Annu Rev Biochem, 74, 535-562.  
15950875 N.Beglova, and S.C.Blacklow (2005).
The LDL receptor: how acid pulls the trigger.
  Trends Biochem Sci, 30, 309-317.  
15494314 N.Beglova, H.Jeon, C.Fisher, and S.C.Blacklow (2004).
Cooperation between fixed and low pH-inducible interfaces controls lipoprotein release by the LDL receptor.
  Mol Cell, 16, 281-292.
PDB code: 1xfe
12857919 E.Neumann, R.Moser, L.Snyers, D.Blaas, and E.A.Hewat (2003).
A cellular receptor of human rhinovirus type 2, the very-low-density lipoprotein receptor, binds to two neighboring proteins of the viral capsid.
  J Virol, 77, 8504-8511.  
14675545 G.Rudenko, and J.Deisenhofer (2003).
The low-density lipoprotein receptor: ligands, debates and lore.
  Curr Opin Struct Biol, 13, 683-689.  
12921543 O.M.Andersen, H.Vorum, B.Honoré, and H.C.Thøgersen (2003).
Ca2+ binding to complement-type repeat domains 5 and 6 from the low-density lipoprotein receptor-related protein.
  BMC Biochem, 4, 7.  
12072496 M.Reithmayer, A.Reischl, L.Snyers, and D.Blaas (2002).
Species-specific receptor recognition by a minor-group human rhinovirus (HRV): HRV serotype 1A distinguishes between the murine and the human low-density lipoprotein receptor.
  J Virol, 76, 6957-6965.  
11258891 N.Beglova, C.L.North, and S.C.Blacklow (2001).
Backbone dynamics of a module pair from the ligand-binding domain of the LDL receptor.
  Biochemistry, 40, 2808-2815.  
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.

 

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