PDBsum entry 1f8z

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protein metals links
Lipid binding protein PDB id
Jmol PyMol
Protein chain
39 a.a. *
* Residue conservation analysis
PDB id:
Name: Lipid binding protein
Title: Nmr structure of the sixth ligand-binding module of the ldl receptor
Structure: Low-density lipoprotein receptor. Chain: a. Fragment: sixth ligand-binding module. Engineered: yes
Source: Synthetic: yes. Other_details: peptide synthesis - based on the human sequence
NMR struc: 20 models
Authors: D.J.Clayton,I.M.Brereton,P.A.Kroon,R.Smith
Key ref:
D.Clayton et al. (2000). Three-dimensional NMR structure of the sixth ligand-binding module of the human LDL receptor: comparison of two adjacent modules with different ligand binding specificities. FEBS Lett, 479, 118-122. PubMed id: 10981718 DOI: 10.1016/S0014-5793(00)01842-1
05-Jul-00     Release date:   18-Oct-00    
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Protein chain
Pfam   ArchSchema ?
P01130  (LDLR_HUMAN) -  Low-density lipoprotein receptor
860 a.a.
39 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure


DOI no: 10.1016/S0014-5793(00)01842-1 FEBS Lett 479:118-122 (2000)
PubMed id: 10981718  
Three-dimensional NMR structure of the sixth ligand-binding module of the human LDL receptor: comparison of two adjacent modules with different ligand binding specificities.
D.Clayton, I.M.Brereton, P.A.Kroon, R.Smith.
The sixth ligand-binding module of the low-density lipoprotein receptor contributes to the binding of apolipoprotein B100-containing lipoproteins. 1H NMR spectroscopy, DYANA and X-PLOR structure calculations were used to determine that this module has a well defined structure with a backbone conformation similar to other modules. Structures from calculations that simulated the presence of a calcium ion showed increased resolution without large increases in energy, increased deviations from idealised geometry or violations of experimental constraints. Investigation of the surface properties of this module indicates there are significant differences from the fifth module, which binds apolipoprotein E-containing lipoproteins in addition to apolipoprotein B100-containing lipoproteins.
  Selected figure(s)  
Figure 2.
Fig. 2. The 20 lowest energy structures of LB6 calculated in (a) the absence of constraints for the calcium ion and (b) the presence of distance constraints for the four conserved acidic residues corresponding to those identified to be equatorial Ca^2+ ligands in LB5. c: Shows secondary structural elements identified in structures shown in (b).
Figure 4.
Fig. 4. Primary sequence and distribution of surface charge and hydrophobicity in LB5 and LB6 (lowest energy structure). Residues shown in bold are common to both modules; residues marked with filled squares are coordinated to calcium in LB5; and those underlined are unique (across all modules) to LB5 between the first and last cysteine residue. Modules in a and d have an similar orientation to that of Fig. 2, then are shown (left to right) rotated in two anticlockwise 90° steps, as viewed from the bottom, around the vertical axis. Positively charged functional groups are shown in blue, negatively charged groups are shown in red, and the sidechains of large non-polar residues (F, I, L, M, V, W) are shown in green.
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2000, 479, 118-122) copyright 2000.  
  Figures were selected by the author.  
    Author's comment    
  See PDB entry 1ldl for the first description of this new fold and the first description of any part of the LDL receptor.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20223219 C.J.Lee, A.De Biasio, and N.Beglova (2010).
Mode of interaction between beta2GPI and lipoprotein receptors suggests mutually exclusive binding of beta2GPI to the receptors and anionic phospholipids.
  Structure, 18, 366-376.
PDB code: 2kri
15952897 H.Jeon, and S.C.Blacklow (2005).
Structure and physiologic function of the low-density lipoprotein receptor.
  Annu Rev Biochem, 74, 535-562.  
15146486 M.Prévost, and V.Raussens (2004).
Apolipoprotein E-low density lipoprotein receptor binding: study of protein-protein interaction in rationally selected docked complexes.
  Proteins, 55, 874-884.  
12429745 A.Li, M.Sadasivam, and J.L.Ding (2003).
Receptor-ligand interaction between vitellogenin receptor (VtgR) and vitellogenin (Vtg), implications on low density lipoprotein receptor and apolipoprotein B/E. The first three ligand-binding repeats of VtgR interact with the amino-terminal region of Vtg.
  J Biol Chem, 278, 2799-2806.  
14675545 G.Rudenko, and J.Deisenhofer (2003).
The low-density lipoprotein receptor: ligands, debates and lore.
  Curr Opin Struct Biol, 13, 683-689.  
14573953 G.Rudenko, L.Henry, C.Vonrhein, G.Bricogne, and J.Deisenhofer (2003).
'MAD'ly phasing the extracellular domain of the LDL receptor: a medium-sized protein, large tungsten clusters and multiple non-isomorphous crystals.
  Acta Crystallogr D Biol Crystallogr, 59, 1978-1986.  
12459547 G.Rudenko, L.Henry, K.Henderson, K.Ichtchenko, M.S.Brown, J.L.Goldstein, and J.Deisenhofer (2002).
Structure of the LDL receptor extracellular domain at endosomal pH.
  Science, 298, 2353-2358.
PDB code: 1n7d
11988467 R.J.Cushley, and M.Okon (2002).
NMR studies of lipoprotein structure.
  Annu Rev Biophys Biomol Struct, 31, 177-206.  
12036962 V.Raussens, C.M.Slupsky, R.O.Ryan, and B.D.Sykes (2002).
NMR structure and dynamics of a receptor-active apolipoprotein E peptide.
  J Biol Chem, 277, 29172-29180.  
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