PDBsum entry 1f8z

Lipid binding protein

PDB id: 1f8z

Contents

Protein chain

39 a.a. *

Metals

_CA

* Residue conservation analysis

PDB id:

1f8z

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

Date:

05-Jul-00 Release date: 18-Oct-00

Protein chain

P01130  (LDLR_HUMAN) -  Low-density lipoprotein receptor from Homo sapiens

Seq: 860 a.a.

Struc: 39 a.a.

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.

ABSTRACT

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.