PDBsum entry: 2fcw

Lipid transport/endocytosis/chaperone

PDB-id: 2fcw

Biological unit* = asymmetric unit, as shown
(*as deduced by PQS)

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Description

Header details

Header records

References

PROCHECK

Protein chains

106 a.a. *

78 a.a. *

Ligands

MPD ×5

Metal ions

_NA ×4

_CA ×2

Waters ×179

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

2fcw

Name:

Lipid transport/endocytosis/chaperone

Title:

Structure of a complex between the pair of the ldl receptor ligand-binding modules 3-4 and the receptor associated protein (rap).

Structure:

Alpha-2-macroglobulin receptor-associated protein. Chain: a. Fragment: domain three. Synonym: alpha-2- mrap, low density lipoprotein receptor- related protein-associated protein 1, rap. Engineered: yes. Mutation: yes. Low-density lipoprotein receptor.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Gene: ldlr.

Biological unit:

Dimer (from PQS)

UniProt:

Chain A: P30533 (AMRP_HUMAN)

Seq:
Struc:
	Seq:	357 a.a.
	Struc:	106 a.a.*

Chain B: P01130 (LDLR_HUMAN)

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

860 a.a.

Struc:

78 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Resolution:

1.26Å

R-factor:

0.152

R-free:

0.201

Authors:

N.Beglova,C.Fisher,S.C.Blacklow

Key ref:

C.Fisher et al. (2006). Structure of an LDLR-RAP complex reveals a general mode for ligand recognition by lipoprotein receptors.. Mol Cell, 22, 277-283. [PubMed id: 16630895] [DOI: 10.1016/j.molcel.2006.02.021]

Date:

12-Dec-05

Release date:

16-May-06

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Clefts

Surface

Key reference

DOI no: 10.1016/j.molcel.2006.02.021

Mol Cell 22:277-283 (2006)

PubMed id: 16630895

Structure of an LDLR-RAP complex reveals a general mode for ligand recognition by lipoprotein receptors.

C.Fisher, N.Beglova, S.C.Blacklow.

ABSTRACT

Proteins of the low-density lipoprotein receptor (LDLR) family are remarkable in their ability to bind an extremely diverse range of protein and lipoprotein ligands, yet the basis for ligand recognition is poorly understood. Here, we report the 1.26 A X-ray structure of a complex between a two-module region of the ligand binding domain of the LDLR and the third domain of RAP, an escort protein for LDLR family members. The RAP domain forms a three-helix bundle with two docking sites, one for each LDLR module. The mode of recognition at each site is virtually identical: three conserved, calcium-coordinating acidic residues from each LDLR module encircle a lysine side chain protruding from the second helix of RAP. This metal-dependent mode of electrostatic recognition, together with avidity effects resulting from the use of multiple sites, represents a general binding strategy likely to apply in the binding of other basic ligands to LDLR family proteins.

Selected figure(s)

Figure 2.
Figure 2. Interface between LA3-4 and RAP-D3

Figure 4.
Figure 4. Docking Model for ApoE Binding

The above figures are reprinted by permission from Cell Press: Mol Cell (2006, 22, 277-283) copyright 2006.

Figures were selected by the author.