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0  structures 672  species 0  interactions 2215  sequences 41  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

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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, the UniProtKB sequence database, 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
(352)
Full
(2215)
Representative proteomes UniProt
(3283)
NCBI
(4240)
Meta
(1)
RP15
(798)
RP35
(1275)
RP55
(1798)
RP75
(2187)
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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
(352)
Full
(2215)
Representative proteomes UniProt
(3283)
NCBI
(4240)
Meta
(1)
RP15
(798)
RP35
(1275)
RP55
(1798)
RP75
(2187)
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
(352)
Full
(2215)
Representative proteomes UniProt
(3283)
NCBI
(4240)
Meta
(1)
RP15
(798)
RP35
(1275)
RP55
(1798)
RP75
(2187)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: 352
Number in full: 2215
Average length of the domain: 67.90 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 36.02 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.8 23.8
Trusted cut-off 23.8 23.8
Noise cut-off 23.7 23.7
Model length: 70
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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