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0  structures 70  species 0  interactions 243  sequences 18  architectures

Family: RHIM (PF12721)

Summary: RIP homotypic interaction motif

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RIP homotypic interaction motif Provide feedback

RIP proteins are receptor-interacting serine/threonine-protein kinases or cell death proteins [1]. This interacting domain is involved in virus recognition. The RHIM domain is necessary for the recruitment of RIP and RIP3 by the IFN-inducible protein DNA-dependent activator of IRFs (DAI), also known as DLM-1 or Z-DNA binding protein (ZBP1). Both the RIP kinases contribute to DAI-induced NF-kappaB activation. RIP3 undergoes auto phosphorylation on binding to DAI [2].

Literature references

  1. Sun X, Yin J, Starovasnik MA, Fairbrother WJ, Dixit VM;, J Biol Chem. 2002;277:9505-9511.: Identification of a novel homotypic interaction motif required for the phosphorylation of receptor-interacting protein (RIP) by RIP3. PUBMED:11734559 EPMC:11734559

  2. Rebsamen M, Heinz LX, Meylan E, Michallet MC, Schroder K, Hofmann K, Vazquez J, Benedict CA, Tschopp J;, EMBO Rep. 2009;10:916-922.: DAI/ZBP1 recruits RIP1 and RIP3 through RIP homotypic interaction motifs to activate NF-kappaB. PUBMED:19590578 EPMC:19590578


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR025735

RIP proteins are receptor-interacting serine/threonine-protein kinases or cell death proteins [PUBMED:11734559]. The RHIM (RIP homotypic interaction motif) domain is involved in virus recognition. It is necessary for the recruitment of RIP and RIP3 by the IFN-inducible protein DNA-dependent activator of IRFs (DAI), also known as DLM-1 or Z-DNA binding protein (ZBP1). Both RIP kinases contribute to DAI-induced NF-kappaB activation. RIP3 undergoes auto phosphorylation on binding to DAI [PUBMED:19590578].

The RHIM domain is also located at the C terminus of TIR-domain-containing adapter-inducing IFN-beta (TRIF). It is essential for TRIF-induced apoptosis, and has been shown to contribute to TRIF-induced NF-kappaB activation [PUBMED:15814722].

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(28)
Full
(243)
Representative proteomes NCBI
(231)
Meta
(2)
RP15
(23)
RP35
(32)
RP55
(39)
RP75
(89)
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Format an alignment

  Seed
(28)
Full
(243)
Representative proteomes NCBI
(231)
Meta
(2)
RP15
(23)
RP35
(32)
RP55
(39)
RP75
(89)
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
(28)
Full
(243)
Representative proteomes NCBI
(231)
Meta
(2)
RP15
(23)
RP35
(32)
RP55
(39)
RP75
(89)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

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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.

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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: Masci AM
Previous IDs: none
Type: Family
Author: Coggill P
Number in seed: 28
Number in full: 243
Average length of the domain: 48.60 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 10.48 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 17.2 5.3
Trusted cut-off 17.2 5.3
Noise cut-off 17.1 5.2
Model length: 53
Family (HMM) version: 2
Download: download the raw HMM for this family

Species distribution

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