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75  structures 1027  species 0  interactions 3489  sequences 45  architectures

Family: Yippee-Mis18 (PF03226)

Summary: Yippee zinc-binding/DNA-binding /Mis18, centromere assembly

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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.

Yippee zinc-binding/DNA-binding /Mis18, centromere assembly Provide feedback

This family includes both Yippee-type proteins and Mis18 kinetochore proteins. Yippee are putative zinc-binding/DNA-binding proteins. Mis18 are proteins involved in the priming of centromeres for recruiting CENP-A. Mis18-alpha and beta form part of a small complex with Mis18-binding protein. Mis18-alpha is found to interact with DNA de-methylases through a Leu-rich region located at its carboxyl terminus [5]. This entry also includes the CULT domain proteins such as Cereblon [6].

Literature references

  1. Roxstrom-Lindquist K, Faye I; , Insect Mol Biol 2001;10:77-86.: The Drosophila gene Yippee reveals a novel family of putative zinc binding proteins highly conserved among eukaryotes. PUBMED:11240639 EPMC:11240639

  2. Berberich SJ, Todd A, Tuttle R;, Front Biosci. 2011;16:1746-1751.: Why YPEL3 represents a novel tumor suppressor. PUBMED:21196260 EPMC:21196260

  3. Fujita Y, Hayashi T, Kiyomitsu T, Toyoda Y, Kokubu A, Obuse C, Yanagida M;, Dev Cell. 2007;12:17-30.: Priming of centromere for CENP-A recruitment by human hMis18alpha, hMis18beta, and M18BP1. PUBMED:17199038 EPMC:17199038

  4. Stimpson KM, Sullivan BA;, Dev Cell. 2012;22:1-2.: Centromeres poised en pointe: CDKs put a hold on CENP-A assembly. PUBMED:22264723 EPMC:22264723

  5. Baumann K;, Nat Rev Mol Cell Biol. 2012;13:340.: Keeping centromeric identity. PUBMED:22552327 EPMC:22552327

  6. Lupas AN, Zhu H, Korycinski M;, PLoS Comput Biol. 2015;11:e1004023.: The thalidomide-binding domain of cereblon defines the CULT domain family and is a new member of the beta-tent fold. PUBMED:25569776 EPMC:25569776


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004910

This domain is found in both Yippee-type proteins and Mis18 kinetochore proteins. Yippee are putative zinc-binding/DNA-binding proteins [PUBMED:11240639]. Mis18 are proteins involved in the priming of centromeres for recruiting CENP-A [PUBMED:17199038, PUBMED:22264723]. Mis18-alpha and beta form part of a small complex with Mis18-binding protein. Mis18-alpha is found to interact with DNA de-methylases through a Leu-rich region located at its carboxyl terminus [PUBMED:22552327]. This domain includes the CULT domain from proteins such as Cereblon [PUBMED:25569776].

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 Beta-tent (CL0080), which has the following description:

This clan contains TCTP, Mss4 and SelR families [1]. The common fold of members of this superfamily has been termed the beta-tent fold [2]. This fold contains two four stranded antiparallel beta sheets. These are oriented at right angles and pinned together at their tip by a zinc ion [2].

The clan contains the following 7 members:

GFA Mss4 NTP_transf_9 RIG-I_C-RD SelR TCTP Yippee-Mis18

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
(47)
Full
(3489)
Representative proteomes UniProt
(4803)
NCBI
(5472)
Meta
(4)
RP15
(835)
RP35
(1889)
RP55
(2816)
RP75
(3378)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(47)
Full
(3489)
Representative proteomes UniProt
(4803)
NCBI
(5472)
Meta
(4)
RP15
(835)
RP35
(1889)
RP55
(2816)
RP75
(3378)
Alignment:
Format:
Order:
Sequence:
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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
(47)
Full
(3489)
Representative proteomes UniProt
(4803)
NCBI
(5472)
Meta
(4)
RP15
(835)
RP35
(1889)
RP55
(2816)
RP75
(3378)
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: Pfam-B_2930 (release 6.5)
Previous IDs: Yippee;
Type: Domain
Sequence Ontology: SO:0000417
Author: Mifsud W
Number in seed: 47
Number in full: 3489
Average length of the domain: 103.00 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 51.16 %

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 26.5 26.5
Trusted cut-off 26.5 26.5
Noise cut-off 26.4 26.4
Model length: 105
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Selections

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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 Yippee-Mis18 domain has been found. There are 75 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 sequence.

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