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0  structures 929  species 0  interactions 3147  sequences 53  architectures

Family: zf-LITAF-like (PF10601)

Summary: LITAF-like zinc ribbon domain

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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.

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

  1. 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

  2. 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

  3. 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

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...

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
(312)
Full
(3147)
Representative proteomes UniProt
(6073)
RP15
(935)
RP35
(1581)
RP55
(2686)
RP75
(3542)
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PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(312)
Full
(3147)
Representative proteomes UniProt
(6073)
RP15
(935)
RP35
(1581)
RP55
(2686)
RP75
(3542)
Alignment:
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Sequence:
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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
(312)
Full
(3147)
Representative proteomes UniProt
(6073)
RP15
(935)
RP35
(1581)
RP55
(2686)
RP75
(3542)
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: Clustering of trematode sequences
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Protasio A , Bateman A
Number in seed: 312
Number in full: 3147
Average length of the domain: 68.00 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 37.27 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.8 23.8
Trusted cut-off 23.8 23.9
Noise cut-off 23.7 23.7
Model length: 70
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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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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
A0A0B4K870 View 3D Structure Click here
A0A0B4K8A8 View 3D Structure Click here
A0A0G2JXT5 View 3D Structure Click here
A0A0J9YTU8 View 3D Structure Click here
A0A1B0GVX0 View 3D Structure Click here
A0A1D6H917 View 3D Structure Click here
A0A2R8RZE9 View 3D Structure Click here
A6H8U1 View 3D Structure Click here
A8DYM6 View 3D Structure Click here
A8JUP5 View 3D Structure Click here
B8A4G9 View 3D Structure Click here
B8A4H0 View 3D Structure Click here
B8A4H1 View 3D Structure Click here
B8A5M5 View 3D Structure Click here
C6SVS5 View 3D Structure Click here
E7FAA1 View 3D Structure Click here
G5EGQ9 View 3D Structure Click here
I1KZF8 View 3D Structure Click here
O61958 View 3D Structure Click here
O61959 View 3D Structure Click here
O62039 View 3D Structure Click here
P0C0T0 View 3D Structure Click here
Q2PE16 View 3D Structure Click here
Q4V6L7 View 3D Structure Click here
Q54HX8 View 3D Structure Click here
Q56VY4 View 3D Structure Click here
Q5U2U6 View 3D Structure Click here
Q67UN6 View 3D Structure Click here
Q6GMG8 View 3D Structure Click here
Q7YTJ4 View 3D Structure Click here
Q7YX40 View 3D Structure Click here
Q7YXD6 View 3D Structure Click here
Q8IRE5 View 3D Structure Click here
Q8MME9 View 3D Structure Click here
Q8T419 View 3D Structure Click here
Q94184 View 3D Structure Click here
Q94CD4 View 3D Structure Click here
Q965P1 View 3D Structure Click here
Q99732 View 3D Structure Click here
Q9DB75 View 3D Structure Click here
Q9H305 View 3D Structure Click here
Q9JLJ0 View 3D Structure Click here
Q9U0H0 View 3D Structure Click here
Q9W1P0 View 3D Structure Click here
Q9W217 View 3D Structure Click here
Q9W219 View 3D Structure Click here
Q9W220 View 3D Structure Click here
Q9W221 View 3D Structure Click here
Q9W222 View 3D Structure Click here
Q9W226 View 3D Structure Click here
Q9W4J2 View 3D Structure Click here
Q9XW97 View 3D Structure Click here
Q9XWU3 View 3D Structure Click here
Q9XWU7 View 3D Structure Click here
Q9XWW3 View 3D Structure Click here

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.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;