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68  structures 1571  species 0  interactions 10036  sequences 183  architectures

Family: Sec23_trunk (PF04811)

Summary: Sec23/Sec24 trunk domain

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.

Sec23/Sec24 trunk domain Provide feedback

COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is known as the trunk domain and has an alpha/beta vWA fold and forms the dimer interface.

Literature references

  1. Lederkremer GZ, Cheng Y, Petre BM, Vogan E, Springer S, Schekman R, Walz T, Kirchhausen T; , Proc Natl Acad Sci USA 2001;98:10704-10709.: Structure of the Sec23p/24p and Sec13p/31p complexes of COPII. PUBMED:11535824 EPMC:11535824


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006896

COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex [ PUBMED:11535824 ]. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation [ PUBMED:12239560 ].

Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger ( INTERPRO ), an alpha/beta trunk domain, an all-helical region ( INTERPRO ), and a C-terminal gelsolin-like domain ( INTERPRO ). This entry describes the Sec23/24 alpha/beta trunk domain, which is formed from a single, approximately 250-residue segment plugged into the beta-barrel between strands beta-1 and beta-19. The trunk has an alpha/beta fold with a vWA topology, and it forms the dimer interface, primarily involving strand beta-14 on Sec23 and Sec24; in addition, the trunk domain of Sec23 contacts Sar1.

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 vWA-like (CL0128), which has the following description:

To add.

The clan contains the following 19 members:

CobT_C Copine DUF1194 DUF2201 DUF444 DUF58 Integrin_beta ivWA Ku_N Med25_VWA Sec23_trunk Ssl1 Ste5_C Tfb4 VWA vWA-TerF-like VWA_2 VWA_3 VWA_CoxE

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 and the UniProtKB 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
(21)
Full
(10036)
Representative proteomes UniProt
(16260)
RP15
(1704)
RP35
(4233)
RP55
(7773)
RP75
(10484)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(21)
Full
(10036)
Representative proteomes UniProt
(16260)
RP15
(1704)
RP35
(4233)
RP55
(7773)
RP75
(10484)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(21)
Full
(10036)
Representative proteomes UniProt
(16260)
RP15
(1704)
RP35
(4233)
RP55
(7773)
RP75
(10484)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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: Bateman A
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 21
Number in full: 10036
Average length of the domain: 235 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 27.41 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 243
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
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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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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 Sec23_trunk domain has been found. There are 68 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044TAZ3 View 3D Structure Click here
A0A044TLC9 View 3D Structure Click here
A0A044UB28 View 3D Structure Click here
A0A077YYD8 View 3D Structure Click here
A0A077ZEA9 View 3D Structure Click here
A0A077ZEJ7 View 3D Structure Click here
A0A0A2V518 View 3D Structure Click here
A0A0B4K5Z8 View 3D Structure Click here
A0A0D2G2T1 View 3D Structure Click here
A0A0D2GBX5 View 3D Structure Click here
A0A0D2GRN7 View 3D Structure Click here
A0A0K0E5F0 View 3D Structure Click here
A0A0K0E8G6 View 3D Structure Click here
A0A0K0EQM8 View 3D Structure Click here
A0A0K0EQU4 View 3D Structure Click here
A0A0N4UB89 View 3D Structure Click here
A0A0P0XNN0 View 3D Structure Click here
A0A0P0Y9Y8 View 3D Structure Click here
A0A0R0I1H8 View 3D Structure Click here
A0A0R4IAZ9 View 3D Structure Click here
A0A0R4ICL5 View 3D Structure Click here
A0A175W4P8 View 3D Structure Click here
A0A1C1CH05 View 3D Structure Click here
A0A1C1CHG4 View 3D Structure Click here
A0A1C1CPF4 View 3D Structure Click here
A0A1D6EFK8 View 3D Structure Click here
A0A1D6EGL6 View 3D Structure Click here
A0A1D6EGS2 View 3D Structure Click here
A0A1D6ERI0 View 3D Structure Click here
A0A1D6FPD9 View 3D Structure Click here
A0A1D6GHW7 View 3D Structure Click here
A0A1D6J6M5 View 3D Structure Click here
A0A1D6L3P4 View 3D Structure Click here
A0A1D8PGX7 View 3D Structure Click here
A0A1D8PJC6 View 3D Structure Click here
A0A1U7F3Y7 View 3D Structure Click here
A0A3P7DBR1 View 3D Structure Click here
A0A3P7DF94 View 3D Structure Click here
A0A3P7FXX9 View 3D Structure Click here
A0A3P7PPM9 View 3D Structure Click here