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2  structures 265  species 0  interactions 323  sequences 15  architectures

Family: SRP-alpha_N (PF04086)

Summary: Signal recognition particle, alpha subunit, N-terminal

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Signal recognition particle, alpha subunit, N-terminal Provide feedback

SRP is a complex of six distinct polypeptides and a 7S RNA that is essential for transferring nascent polypeptide chains that are destined for export from the cell to the translocation apparatus of the endoplasmic reticulum (ER) membrane [1]. SRP binds hydrophobic signal sequences as they emerge from the ribosome, and arrests translation.

Literature references

  1. Matlin KS; , Nat Rev Mol Cell Biol 2002;3:538-542.: Timeline: The strange case of the signal recognition particle. PUBMED:12094220 EPMC:12094220


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007222

The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [PUBMED:17622352, PUBMED:16469117]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor [PUBMED:17507650]. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 [PUBMED:12364595].

The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain [PUBMED:12654246]. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon [PUBMED:10859309]. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane [PUBMED:7844142]. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel.

This entry represents the alpha subunit of the SR receptor.

Gene Ontology

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Domain organisation

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Alignments

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(27)
Full
(323)
Representative proteomes NCBI
(320)
Meta
(1)
RP15
(80)
RP35
(131)
RP55
(196)
RP75
(237)
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Format an alignment

  Seed
(27)
Full
(323)
Representative proteomes NCBI
(320)
Meta
(1)
RP15
(80)
RP35
(131)
RP55
(196)
RP75
(237)
Alignment:
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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
(27)
Full
(323)
Representative proteomes NCBI
(320)
Meta
(1)
RP15
(80)
RP35
(131)
RP55
(196)
RP75
(237)
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.

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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.

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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_7342 (release 7.3);
Previous IDs: none
Type: Family
Author: Wood V, Finn RD
Number in seed: 27
Number in full: 323
Average length of the domain: 243.40 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 40.50 %

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 25.4 25.4
Trusted cut-off 25.7 25.4
Noise cut-off 24.8 25.3
Model length: 279
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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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 SRP-alpha_N domain has been found. There are 2 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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