SUPERFAMILY 1.73 HMM library and genome assignments server


LDL receptor-like module superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (85)
  Usually dominated by metal ligand, heme, and/or disulfide bridges
Fold:   LDL receptor-like module [ 57423]
  disulfide-rich calcium-binding fold
Superfamily:   LDL receptor-like module [ 57424]
Families:   LDL receptor-like module [ 57425] (6)


Superfamily statistics
Genomes (97) UniProt 15.0 PDB chains (SCOP 1.73)
Domains 17,213 6,664 24
Proteins 4,138 1,712 18


Functional annotation
General category Processes_IC
Detailed category Transport

Function annotation of SCOP domain superfamilies
InterPro annotation
Cross references IPR002172 SSF57424 Protein matches
Abstract

Low density lipoprotein (LDL) is the major cholesterol-carrying lipoprotein of plasma. The receptor protein binds LDL and transports it into cells by endocytosis. In order to be internalised, the receptor-ligand complex must first cluster into clathrin-coated pits. Seven successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein [PubMed6091915].

The LDL-receptor class A domain contains 6 disulphide-bound cysteines [PubMed7548065] and a highly conserved cluster of negatively charged amino acids, of which many are clustered on one face of the module [PubMed7603991]. A schematic representation of this domain is shown here:

   +---------------------+        +--------------------------------+
   |                     |        |                                |
  -CxxxxxxxxxxxxCxxxxxxxxCxxxxxxxxCxxxxxxxxxxCxxxxxxxxxxxxxxxxxxxxxC-
                |                            |
                +----------------------------+

'C': conserved cysteine involved in a disulphide bond.
'x': any residue.

In LDL-receptors the class A domains form the binding site for LDL [PubMed6091915] and calcium [PubMed3320043]. The acidic residues between the fourth and sixth cysteines are important for high-affinity binding of positively charged sequences in LDLR's ligands [PubMed3283935]. The repeat has been shown [PubMed7603991] to consist of a beta-hairpin structure followed by a series of beta turns. In the absence of calcium, LDL-A domains are unstructured; the bound calcium ion imparts structural integrity.

Following these repeats is a 350 residue domain that resembles part of the epidermal growth factor (EGF) precursor [PubMed6327078, PubMed6091915].

Similar domains have been found (see references in [PubMed7603991]) in several extracellular and membrane proteins (see examples).

Numerous familial hypercholestorolemia mutations of the LDL receptor alter the calcium coordinating residue of LDL-A domains or other crucial scaffolding residues.


InterPro database

PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

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Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 15 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a LDL receptor-like module domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 15 hidden Markov models representing the LDL receptor-like module superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Internal database links ]