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45  structures 319  species 1  interaction 975  sequences 9  architectures

Family: HORMA (PF02301)

Summary: HORMA domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "HORMA domain". More...

HORMA domain Edit Wikipedia article

HORMA domain
PDB 1go4 EBI.jpg
crystal structure of mad1-mad2 reveals a conserved mad2 binding motif in mad1 and cdc20.
Identifiers
Symbol HORMA
Pfam PF02301
InterPro IPR003511
SCOP 1duj
SUPERFAMILY 1duj

In molecular biology, the HORMA domain (named after the Hop1p, Rev7p and MAD2 proteins) is a protein domain that has been suggested to recognise chromatin states resulting from DNA adducts, double stranded breaks or non-attachment to the spindle and act as an adaptor that recruits other proteins. Hop1 is a meiosis-specific protein, Rev7 is required for DNA damage induced mutagenesis, and MAD2 is a spindle checkpoint protein which prevents progression of the cell cycle upon detection of a defect in mitotic spindle integrity.[1][2]

Examples[edit]

Humans proteins containing this domain include:

References[edit]

External links[edit]

This article incorporates text from the public domain Pfam and InterPro IPR003511

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

HORMA domain Provide feedback

The HORMA (for Hop1p, Rev7p and MAD2) domain has been suggested to recognise chromatin states that result from DNA adducts, double stranded breaks or non-attachment to the spindle and acts as an adaptor that recruits other proteins. MAD2 is a spindle checkpoint protein which prevents progression of the cell cycle upon detection of a defect in mitotic spindle integrity.

Literature references

  1. He X, Patterson TE, Sazer S; , Proc Natl Acad Sci U S A 1997;94:7965-7970.: The Schizosaccharomyces pombe spindle checkpoint protein mad2p blocks anaphase and genetically interacts with the anaphase-promoting complex. PUBMED:9223296 EPMC:9223296

  2. Aravind L, Koonin EV; , Trends Biochem Sci 1998;23:284-286.: The HORMA domain: a common structural denominator in mitotic checkpoints, chromosome synapsis and DNA repair. PUBMED:9757827 EPMC:9757827


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003511

The HORMA (for Hop1p, Rev7p and MAD2) domain has been suggested to recognise chromatin states that result from DNA adducts, double stranded breaks or non-attachment to the spindle and acts as an adaptor that recruits other proteins. Hop1 is a meiosis-specific protein, Rev7 is required for DNA damage induced mutagenesis, and MAD2 is a spindle checkpoint protein which prevents progression of the cell cycle upon detection of a defect in mitotic spindle integrity [PUBMED:9757827, PUBMED:9223296].

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(95)
Full
(975)
Representative proteomes NCBI
(916)
Meta
(11)
RP15
(196)
RP35
(321)
RP55
(493)
RP75
(638)
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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
(95)
Full
(975)
Representative proteomes NCBI
(916)
Meta
(11)
RP15
(196)
RP35
(321)
RP55
(493)
RP75
(638)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(95)
Full
(975)
Representative proteomes NCBI
(916)
Meta
(11)
RP15
(196)
RP35
(321)
RP55
(493)
RP75
(638)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: [2]
Previous IDs: MAD2;
Type: Domain
Author: Bateman A, Mian N
Number in seed: 95
Number in full: 975
Average length of the domain: 183.40 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 60.33 %

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 20.7 20.7
Trusted cut-off 20.9 20.8
Noise cut-off 20.5 20.0
Model length: 208
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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Interactions

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

HORMA

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 HORMA domain has been found. There are 45 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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