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131  structures 152  species 9  interactions 2061  sequences 79  architectures

Family: Recep_L_domain (PF01030)

Summary: Receptor L domain

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Receptor L domain Provide feedback

The L domains from these receptors make up the bilobal ligand binding site. Each L domain consists of a single-stranded right hand beta-helix [1]. This Pfam entry is missing the first 50 amino acid residues of the domain.

Literature references

  1. Garrett TP, McKern NM, Lou M, Frenkel MJ, Bentley JD, Lovrecz GO, Elleman TC, Cosgrove LJ, Ward CW; , Nature 1998;394:395-399.: Crystal structure of the first three domains of the type-1 insulin-like growth factor receptor. PUBMED:9690478 EPMC:9690478


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000494

The structure for the first three domains of the extracellular portion of IGF-1R (type-1 insulin-like growth-factor receptor) has been solved and consists of two L-domains and a cysteine rich region (L1-Cys-rich-L2). The L-domains each consist of a single-stranded right-handed beta-helix. The Cys-rich region is composed of eight disulphide-bonded modules, seven of which form a rod-shaped domain with modules associated in an unusual manner. The three domains surround a central space of sufficient size to accommodate a ligand molecule [PUBMED:9690478].

This entry represents the L-domain. This domain can also be found in insulin receptor(IR) and epidermal growth-factor receptor (EGFR) family members, and in yeast cell surface GPI proteins PST1 and ECM33 [PUBMED:15583168].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan LRR (CL0022), which has the following description:

Each Leucine Rich Repeat is composed of a beta-alpha unit. These units form elongated non-globular structures. Leucine Rich Repeats are often flanked by cysteine rich domains. This Pfam entry contains Leucine Rich Repeats not recognised by the Pfam:PF00560 model.

The clan contains the following 11 members:

DUF285 FNIP LRR_1 LRR_2 LRR_3 LRR_4 LRR_5 LRR_6 LRR_8 LRR_9 Recep_L_domain

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(53)
Full
(2061)
Representative proteomes UniProt
(3916)
NCBI
(6452)
Meta
(28)
RP15
(433)
RP35
(642)
RP55
(1448)
RP75
(1742)
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PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(53)
Full
(2061)
Representative proteomes UniProt
(3916)
NCBI
(6452)
Meta
(28)
RP15
(433)
RP35
(642)
RP55
(1448)
RP75
(1742)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(53)
Full
(2061)
Representative proteomes UniProt
(3916)
NCBI
(6452)
Meta
(28)
RP15
(433)
RP35
(642)
RP55
(1448)
RP75
(1742)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_244 (release 3.0)
Previous IDs: none
Type: Domain
Author: Finn RD, Bateman A
Number in seed: 53
Number in full: 2061
Average length of the domain: 112.80 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 21.65 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.8 21.8
Trusted cut-off 21.8 21.8
Noise cut-off 21.7 21.7
Model length: 112
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Interactions

There are 9 interactions for this family. More...

EGF Furin-like Recep_L_domain V-set GF_recep_IV Furin-like Insulin Insulin B

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Recep_L_domain domain has been found. There are 131 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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