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19  structures 1915  species 2  interactions 3603  sequences 54  architectures

Family: SCP2 (PF02036)

Summary: SCP-2 sterol transfer family

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This is the Wikipedia entry entitled "Sterol carrier protein". More...

Sterol carrier protein Edit Wikipedia article

1c44.gif
Sterol carrier protein 2
Identifiers
Symbol SCP2
Pfam PF02036
InterPro IPR003033
PROSITE PDOC00092
SCOP 1qnd
SUPERFAMILY 1qnd
OPM superfamily 144
OPM protein 2cx7

Sterol carrier proteins (also known as nonspecific lipid transfer proteins) is a family of proteins that transfer steroids and probably also phospholipids and gangliosides between cellular membranes.

These proteins are different from plant nonspecific lipid transfer proteins but structurally similar to small proteins of unknown function from Thermus thermophilus.

This domain is involved in binding sterols. The human sterol carrier protein 2 (SCP2) is a basic protein that is believed to participate in the intracellular transport of cholesterol and various other lipids.[1]

Contents

[edit] Human proteins containing this domain

HSD17B4; HSDL2; SCP2; STOML1;

[edit] See also

[edit] References

  1. ^ Johansson J, Wuthrich K, Szyperski T, Scheek S, Assmann G, Seedorf U (1993). "NMR determination of the secondary structure and the three-dimensional polypeptide backbone fold of the human sterol carrier protein 2". FEBS Lett. 335 (1): 18–26. doi:10.1016/0014-5793(93)80431-S. PMID 8243660.

[edit] External links

This article incorporates text from the public domain Pfam and InterPro IPR003033


This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

SCP-2 sterol transfer family Provide feedback

This domain is involved in binding sterols. It is found in the SCP2 protein P22307 as well as the C terminus of P51659 the enzyme estradiol 17 beta-dehydrogenase EC:1.1.1.62. The UNC-24 protein Q17372 contains an SPFH domain PF01145 [2].

Literature references

  1. Szyperski T, Scheek S, Johansson J, Assmann G, Seedorf U, Wuthrich K; , FEBS Lett 1993;335:18-26.: NMR determination of the secondary structure and the three-dimensional polypeptide backbone fold of the human sterol carrier protein 2. PUBMED:8243660 EPMC:8243660

  2. Barnes TM, Jin Y, Horvitz HR, Ruvkun G, Hekimi S; , J Neurochem 1996;67:46-57.: The Caenorhabditis elegans behavioral gene unc-24 encodes a novel bipartite protein similar to both erythrocyte band 7.2 (stomatin) and nonspecific lipid transfer protein. PUBMED:8667025 EPMC:8667025


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003033

This domain is involved in binding sterols, and is found in proteins such as SCP2. This domain has a 3-layer alpha/beta/alpha fold, composed of alpha/beta(3)/(crossover)/beta/(alpha)/beta.

The human sterol carrier protein 2 (SCP2) is a basic protein that is believed to participate in the intracellular transport of cholesterol and various other lipids [PUBMED:8243660]. The Unc-24 protein of Caenorhabditis elegans contains a domain similar to part of two ion channel regulators (the erythrocyte integral membrane protein stomatin and the C. elegans neuronal protein MEC-2) juxtaposed to a domain similar to nonspecific lipid transfer protein (nsLTP; also called sterol carrier protein 2) [PUBMED:8667025].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 SCP2 (CL0311), which has the following description:

This superfamily includes the SCP2 family as well as a domain from the mycothiol dependent maleylpyruvate isomerase.

The clan contains the following 3 members:

Alkyl_sulf_C MDMPI_C SCP2

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(174)
Full
(3603)
Representative proteomes NCBI
(2747)
Meta
(690)
RP15
(351)
RP35
(606)
RP55
(884)
RP75
(1132)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(174)
Full
(3603)
Representative proteomes NCBI
(2747)
Meta
(690)
RP15
(351)
RP35
(606)
RP55
(884)
RP75
(1132)
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
(174)
Full
(3603)
Representative proteomes NCBI
(2747)
Meta
(690)
RP15
(351)
RP35
(606)
RP55
(884)
RP75
(1132)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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_1050 (Release 5.1)
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 174
Number in full: 3603
Average length of the domain: 100.00 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 46.14 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.3 21.3
Trusted cut-off 21.3 21.3
Noise cut-off 21.2 21.2
Model length: 102
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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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 2 interactions for this family. More...

SCP2 TPR_1

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 SCP2 domain has been found. There are 19 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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