Summary: LITAF-like zinc ribbon domain
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LITAF-like zinc ribbon domain Provide feedback
Members of this family display a conserved zinc ribbon structure [1] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS)[2]. The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [3].
Literature references
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Krishna SS, Majumdar I, Grishin NV; , Nucleic Acids Res. 2003;31:532-550.: Structural classification of zinc fingers: survey and summary. PUBMED:12527760 EPMC:12527760
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Yu Y, Qiu L, Song L, Zhao J, Ni D, Zhang Y, Xu W; , Fish Shellfish Immunol. 2007;23:419-429.: Molecular cloning and characterization of a putative lipopolysaccharide-induced TNF-alpha factor (LITAF) gene homologue from Zhikong scallop Chlamys farreri. PUBMED:17408970 EPMC:17408970
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Ponting CP, Mott R, Bork P, Copley RR; , Genome Res 2001;11:1996-2008.: Novel protein domains and repeats in Drosophila melanogaster: insights into structure, function, and evolution. PUBMED:11731489 EPMC:11731489
Internal database links
Similarity to PfamA using HHSearch: | zinc_ribbon_15 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR006629
LITAF (LPS-induced TNF-activating factor) (also known as SIMPLE; small integral membrane protein of the late endosome) is an endosome-associated integral membrane protein important for multivesicular body (MVB) sorting. It is a monotypic membrane protein with both termini exposed to the cytoplasm and is anchored to membranes via an in-plane helical membrane anchor, present within the highly conserved C-terminal region known as the 'LITAF domain' or 'SIMPLE-like domain'. The LITAF domain consists of conserved cysteines separated by a 22 residue hydrophobic region. LITAF domains are found throughout the eukaryotes, suggesting ancient conserved functions, with multiple instances of expansion, especially in the metazoa [ PUBMED:27582497 , PUBMED:27927196 ].
The LITAF domain consists of five beta-sheets, three N-terminal and two C- terminal to the predicted hydrophobic anchor region and is stabilized by the coordination of a zinc atom by two pairs of evolutionarily conserved cysteine residues. Consistent with a protein domain that resides in close proximity to membranes, specific residues within the LITAF domain interact with phosphoethanolamine (PE) head groups. The anchoring-region of the LITAF domain is likely to embed into the cytosolic-facing monolayer of the membrane bilayer by adopting an amphipathic character [ PUBMED:27927196 ].
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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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...
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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.
Seed (306) |
Full (3702) |
Representative proteomes | UniProt (6505) |
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RP15 (1092) |
RP35 (1825) |
RP55 (3013) |
RP75 (3930) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (306) |
Full (3702) |
Representative proteomes | UniProt (6505) |
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RP15 (1092) |
RP35 (1825) |
RP55 (3013) |
RP75 (3930) |
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Raw Stockholm | |||||||
Gzipped |
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
Seed source: | Clustering of trematode sequences |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Protasio A |
Number in seed: | 306 |
Number in full: | 3702 |
Average length of the domain: | 68.2 aa |
Average identity of full alignment: | 29 % |
Average coverage of the sequence by the domain: | 38.05 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 70 | ||||||||||||
Family (HMM) version: | 12 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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.
trRosetta Structure
The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.
The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.
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