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70  structures 1570  species 0  interactions 8970  sequences 153  architectures

Family: zf-Sec23_Sec24 (PF04810)

Summary: Sec23/Sec24 zinc finger

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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.

Sec23/Sec24 zinc finger 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 found to be zinc binding domain.

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 IPR006895

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [ PUBMED:10529348 , PUBMED:15963892 , PUBMED:15718139 , PUBMED:17210253 , PUBMED:12665246 ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few [ PUBMED:11179890 ]. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.

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, an alpha/beta trunk domain ( INTERPRO ), an all-helical region ( INTERPRO ), and a C-terminal gelsolin-like domain ( INTERPRO ). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex.

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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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...

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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.

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

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

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Representative proteomes UniProt

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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.

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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...


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: 300
Number in full: 8970
Average length of the domain: 39 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 4.34 %

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 25.0 25.0
Trusted cut-off 25.0 25.0
Noise cut-off 24.9 24.9
Model length: 39
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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


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


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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 zf-Sec23_Sec24 domain has been found. There are 70 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
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
A0A0N4UN01 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
A0A1D6GHW7 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
A0A3Q0KJQ2 View 3D Structure Click here
A0A5K4EIV9 View 3D Structure Click here