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10  structures 129  species 1  interaction 552  sequences 17  architectures

Family: CIDE-N (PF02017)

Summary: CIDE-N domain

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CIDE-N domain Provide feedback

This domain is found in CAD nuclease O76075 , ICAD O00273 the inhibitor of CAD nuclease. The two proteins interact through this domain.

Literature references

  1. Enari M, Sakahira H, Yokoyama H, Okawa K, Iwamatsu A, Nagata S; , Nature 1998;391:43-50.: A caspase-activated DNase that degrades DNA during apoptosis, and its inhibitor ICAD [see comments] [published erratum appears in Nature 1998 May 28;393(6683):396] PUBMED:9422506 EPMC:9422506

  2. Sakahira H, Enari M, Nagata S; , Nature 1998;391:96-99.: Cleavage of CAD inhibitor in CAD activation and DNA degradation during apoptosis [see comments] PUBMED:9422513 EPMC:9422513

  3. Lugovskoy AA, Zhou P, Chou JJ, McCarty JS, Li P, Wagner G; , Cell 1999;99:747-755.: Solution structure of the CIDE-N domain of CIDE-B and a model for CIDE- N/CIDE-N interactions in the DNA fragmentation pathway of apoptosis [In Process Citation] PUBMED:10619428 EPMC:10619428


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003508

The CIDE-N or CAD domain is a ~78 amino acid protein-protein interaction domain in the N-terminal part of Cell death-Inducing DFF45-like Effector (CIDE) proteins, involved in apoptosis. At the final stage of programmed cell death, chromosomal DNA is degraded into fragments by Caspase-activated DNase (CAD), also named DNA fragmentation factor 40 kDa (DFF40). In normal cells CAD/DFF40 is completely inhibited by its binding to DFF45 or Inhibitor of CAD (ICAD). Apoptotic stimuli provoke cleavage of ICAD/DFF45 by caspases, resulting in self-assembly of CAD/DFF40 into the active dimer [PUBMED:15149602].

Both CAD/DFF40 and ICAD/DFF45 possess an N-terminal CIDE-N domain that is involved in their interaction. The name of the CIDE-N domain refers to the CIDE proteins and CAD, where the domain forms the N-terminal part [PUBMED:9564035, PUBMED:10619428]. The CIDE-N domains from different proteins can interact, e.g. CIDE-N of CIDE-B and ICAD/DFF45 with CIDE-N of CAD/DFF40, and such interactions can also be needed for proper folding [PUBMED:10764577, PUBMED:11371636].

Tertiary structures show that the CIDE-N domain forms an alpha/beta roll fold of five beta-strands forming a single, mixed parallel/anti-parallel beta-sheet with one [PUBMED:10764577] or two [PUBMED:10619428, PUBMED:11371636] alpha-helices packed against the sheet. Binding surfaces of the CIDE-N domain form a central hydrophobic cluster, while specific binding interfaces can be formed by charged patches.

Some proteins known to contain a CIDE-N domain include:

  • Mammalian DNA fragmentation factor 40 kDa (DFF40) or Caspase-activated deoxyribonuclease (CAD), an endonuclease that induces DNA fragmentation and chromatin condensation during apoptosis. The degradation of chromosomal DNA by CAD/DFF40 will kill the cells.
  • Mammalian DNA fragmentation factor 45 kDa (DFF45) or Inhibitor of CAD (ICAD), which controls the activity and proper folding of CAD/DFF40.
  • Mammalian CIDE-A and CIDE-B, activators of cell death and DNA fragmentation that can be inhibited by ICAD/DFF45. In contrast with CAD and ICAD, the CIDE proteins are expressed in a highly restricted way and show pronounced tissue specificity.
  • Fruit fly DNAation factor DREP1, a DFF45 homologue that can inhibit CIDE-A-induced apoptosis.

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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Pfam Clan

This family is a member of clan Ubiquitin (CL0072), which has the following description:

This family includes proteins that share the ubiquitin fold. It currently unites four SCOP superfamilies.

The clan contains the following 40 members:

APG12 Atg8 Blt1 Caps_synth_GfcC CIDE-N Cobl DUF2407 DUF4430 DWNN FERM_N Lambda_tail_I Multi_ubiq NQRA_SLBB PB1 PI3K_rbd Plug Prok_Ub RA Rad60-SLD Rad60-SLD_2 Ras_bdg_2 RBD SLBB Telomere_Sde2 TGS ThiS ThiS-like TmoB TUG-UBL1 Ub-Mut7C Ub-RnfH ubiquitin Ubiquitin_2 Ubiquitin_3 UBX Ufm1 UN_NPL4 Urm1 YchF-GTPase_C YukD

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.

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(100)
Full
(552)
Representative proteomes NCBI
(925)
Meta
(0)
RP15
(51)
RP35
(109)
RP55
(212)
RP75
(330)
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Key: ✓ available, x not generated, not available.

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  Seed
(100)
Full
(552)
Representative proteomes NCBI
(925)
Meta
(0)
RP15
(51)
RP35
(109)
RP55
(212)
RP75
(330)
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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
(100)
Full
(552)
Representative proteomes NCBI
(925)
Meta
(0)
RP15
(51)
RP35
(109)
RP55
(212)
RP75
(330)
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.

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.

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: [3]
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 100
Number in full: 552
Average length of the domain: 73.30 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 24.20 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.8 21.8
Trusted cut-off 21.9 22.6
Noise cut-off 21.5 21.5
Model length: 76
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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Interactions

There is 1 interaction for this family. More...

CIDE-N

Structures

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 CIDE-N domain has been found. There are 10 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 seqence.

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