Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
13  structures 787  species 3  interactions 956  sequences 10  architectures

Family: Sec61_beta (PF03911)

Summary: Sec61beta family

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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.

Sec61beta family Provide feedback

This family consists of homologues of Sec61beta - a component of the Sec61/SecYEG protein secretory system. The domain is found in eukaryotes and archaea and is possibly homologous to the bacterial SecG. It consists of a single putative transmembrane helix, preceded by a short stretch containing various charged residues; this arrangement may help determine orientation in the cell membrane [1].

Literature references

  1. Kinch LN, Saier MH Jr, Grishin NV; , Trends Biochem Sci 2002;27:170-171.: Sec61beta - a component of the archaeal protein secretory system. PUBMED:11943537 EPMC:11943537


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR016482

This family includes preprotein translocase subunit SecG, protein transport protein Sec61 subunit beta and Sbh1.

A conserved heterotrimeric integral membrane protein complex--the Sec61 complex (eukaryotes) or SecY complex (prokaryotes)--forms a protein-conducting channel that allows polypeptides to be transferred across (or integrated into) the endoplasmic reticulum (eukaryotes) or across the cytoplasmic membrane (prokaryotes) [PUBMED:14661030, PUBMED:11597451]. This complex is itself a part of a larger translocase complex.

The alpha subunits (INTERPRO), called Sec61alpha in mammals, Sec61p in Saccharomyces cerevisiae (Baker's yeast), and SecY in prokaryotes, and the gamma subunits ( and ), called Sec61gamma in mammals, Sss1p in S. cerevisiae, and SecE in prokaryotes, show significant sequence conservation. Both subunits are required for cell viability in S. cerevisiae and Escherichia coli. The beta subunits, called Sec61beta in mammals, Sbh in S. cerevisiae, and Sec-beta in archaea (), are not essential for cell viability; they are similar in eukaryotes and archaea, but show no obvious homology to the corresponding SecG subunits () in bacteria. SecY forms the channel pore, and it is the cross-linking partner of polypeptide chains passing through the membrane [PUBMED:14661030]. SecY and SecE constitute the high-affinity SecA-binding site on the membrane [PUBMED:11597451].

The channel is a passive conduit for polypeptides. It must therefore associate with other components that provide a driving force. The partner proteins in bacteria and eukaryotes differ. In bacteria, the translocase complex comprises 7 proteins [PUBMED:14661030], including a chaperone protein (SecB; ), an ATPase (SecA; ), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD; and SecF; ). The SecA ATPase interacts dynamically with the SecYEG integral membrane components to drive the transmembrane movement of newly synthesized preproteins [PUBMED:11597451]. In S. cerevisiae (and probably in all eukaryotes), the full translocase comprises another membrane protein subcomplex (the tetrameric Sec62/63p complex), and the lumenal protein BiP, a member of the Hsp70 family of ATPases. BiP promotes translocation by acting as a molecular ratchet, preventing the polypeptide chain from sliding back into the cytosol [PUBMED:14661030].

Domain organisation

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

Loading domain graphics...

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
(123)
Full
(956)
Representative proteomes NCBI
(823)
Meta
(55)
RP15
(126)
RP35
(286)
RP55
(428)
RP75
(533)
Jalview View  View  View  View  View  View  View  View 
HTML View  View  View  View  View  View     
PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

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

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

Format an alignment

  Seed
(123)
Full
(956)
Representative proteomes NCBI
(823)
Meta
(55)
RP15
(126)
RP35
(286)
RP55
(428)
RP75
(533)
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
(123)
Full
(956)
Representative proteomes NCBI
(823)
Meta
(55)
RP15
(126)
RP35
(286)
RP55
(428)
RP75
(533)
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.

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: [1]
Previous IDs: none
Type: Family
Author: Yeats C
Number in seed: 123
Number in full: 956
Average length of the domain: 39.10 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 39.91 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 19.8 19.8
Trusted cut-off 19.9 20.0
Noise cut-off 19.7 19.7
Model length: 40
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Interactions

There are 3 interactions for this family. More...

SecE Plug_translocon SecY

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 Sec61_beta domain has been found. There are 13 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.

Loading structure mapping...