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218  structures 1562  species 0  interactions 31052  sequences 970  architectures

Family: Chromo (PF00385)

Summary: Chromo (CHRromatin Organisation MOdifier) 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 "Chromodomain". More...

Chromodomain Edit Wikipedia article

A chromodomain a is protein structural domain of about 40-50 amino acid residues commonly found in proteins associated with the remodeling and manipulation of chromatin. The domain is highly conserved among both plants and animals, and is represented in a large number of different proteins in many genomes, such as that of the mouse. Some chromodomain-containing genes have multiple alternative splicing isoforms that omit the chromodomain entirely.[1] In mammals, chromdomain-containing proteins are responsible for aspects of gene regulation related to chromatin remodeling and formation of heterochromatin regions.[2] Chromodomain-containing proteins also bind methylated histones[3][4] and appear in the RNA-induced transcriptional silencing complex.[5]


  1. ^ Tajul-Arifin K, Teasdale R, Ravasi T, Humel DA, RIKEN GER Group, GSL Members, Mattick JS. (2003). Identification and Analysis of Chromodomain-Containing Proteins Encoded in the Mouse Transcriptome. Genome Res 13:1416-1429. PMID 12819141
  2. ^ Jones DO, Cowell IG, Singh PB. (2000). Mammalian chromodomain proteins: their role in genome organisation and expression. Bioessays 22(2):124-37. PMID 10655032
  3. ^ Nielsen PR, Nietlispach D, Mott HR, Callaghan J, Bannister A, Kouzarides T, Murzin AG, Murzina NV, Laue ED. (2002). Structure of the HP1 chromodomain bound to histone H3 methylated at lysine 9. Nature 416(6876):103-7. PMID 11882902
  4. ^ Jacobs SA, Khorasanizadeh S. (2002). Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail. Science 295(5562):2080-3. PMID 11859155
  5. ^ Verdel A, Jia S, Gerber S, Sugiyama T, Gygi S, Grewal S, Moazed D (2004). "RNAi-mediated targeting of heterochromatin by the RITS complex". Science 303 (5658): 672-6. PMID 14704433.

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.

Chromo (CHRromatin Organisation MOdifier) domain Provide feedback

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Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR023780

The CHROMO (CHRromatin Organization MOdifier) domain [ PUBMED:1982376 , PUBMED:1708124 , PUBMED:7667093 , PUBMED:7501439 ] is a conserved region of around 60 amino acids, originally identified in Drosophila modifiers of variegation. These are proteins that alter the structure of chromatin to the condensed morphology of heterochromatin, a cytologically visible condition where gene expression is repressed. In one of these proteins, Polycomb, the chromo domain has been shown to be important for chromatin targeting.

Proteins that contain a chromo domain appear to fall into 3 classes. The first class includes proteins having an N-terminal chromo domain followed by a region termed the chromo shadow domain, with weak but significant sequence similarity to the N-terminal chromo domain,[ PUBMED:7667093 ], eg. Drosophila and human heterochromatin protein Su(var)205 (HP1). The second class includes proteins with a single chromo domain, eg. Drosophila protein Polycomb (Pc); mammalian modifier 3; human Mi-2 autoantigen and several yeast and Caenorhabditis elegans hypothetical proteins. In the third class paired tandem chromo domains are found, eg. in mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1.

Functional dissections of chromo domain proteins suggests a mechanistic role for chromo domains in targeting chromo domain proteins to specific regions of the nucleus. The mechanism of targeting may involve protein-protein and/or protein/nucleic acid interactions. Hence, several line of evidence show that the HP1 chromo domain is a methyl-specific histone binding module, whereas the chromo domain of two protein components of the drosophila dosage compensation complex, MSL3 and MOF, contain chromo domains that bind to RNA in vitro [ PUBMED:11574148 ].

The high resolution structures of HP1-family protein chromo and chromo shadow domain reveal a conserved chromo domain fold motif consisting of three beta strands packed against an alpha helix. The chromo domain fold belongs to the OB (oligonucleotide/oligosaccharide binding)-fold class found in a variety of prokaryotic and eukaryotic nucleic acid binding protein [ PUBMED:11574148 ].

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 Tudor (CL0049), which has the following description:

This clan covers the Tudor domain 'royal family' [1]. This includes chromo, MBT, PWWP and tudor domains. The chromo domain is a comprised of approximately 50 amino acid residues. There are usually one to three Chromo domains found in a single protein. In some chromo domain containing proteins, a second related chromo domain has been found and is referred to as the Chromo-shadow domain. The structure of the Chromo and Chromo-shadow domains reveal an OB-fold, a fold found in a variety of prokaryotic and eukaryotic nucleic acid binding proteins. More specifically,the chromo-domain structure reveals a three beta strands that are packed against an alpha helix. Interestingly, a similar structure is found in the archaeal chromatin proteins (7kDa DNA-binding domain). These are sequence neutral DNA binding proteins. The DNA binding in these archaeal proteins is mediated through the triple stranded beta sheet. These archaeal domains are though to represent an ancestral chromo domain. Homologs of the chromo domain have been found in fission yeast, ciliated protozoa and all animal species, but appear to be absent in eubacteria, budding yeast and plants [2]. The precise function of the chromo domain is unclear, but the chromo domain is thought to act as a targeting module for chromosomal proteins, although the chromosomal contexts and functional contexts being targeted vary. In all cases studies, the chromo domains are found in proteins that are involved in transcription regulation, positive and negative [2].

The clan contains the following 33 members:

53-BP1_Tudor 7kD_DNA_binding Agenet Chromo Chromo_2 Chromo_shadow Cul7 DUF1325 DUF4537 DUF4819 GEN1_C Hva1_TUDOR LBR_tudor LytTR MBT Mtf2_C ProQ_C PWWP Rad9_Rad53_bind RBB1NT SAWADEE SMN SNase TTD TUDOR Tudor-knot Tudor_1_RapA Tudor_2 Tudor_3 Tudor_4 Tudor_5 Tudor_FRX1 Tudor_RapA


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 and the UniProtKB 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.

Representative proteomes UniProt
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Representative proteomes UniProt

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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.

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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...


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: Prosite
Previous IDs: chromo;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 82
Number in full: 31052
Average length of the domain: 54.8 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 6.32 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.1 25.1
Trusted cut-off 25.1 25.1
Noise cut-off 25.0 25.0
Model length: 54
Family (HMM) version: 27
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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 Chromo domain has been found. There are 218 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044RKZ3 View 3D Structure Click here
A0A044SBW8 View 3D Structure Click here
A0A044SPF7 View 3D Structure Click here
A0A044UQ51 View 3D Structure Click here
A0A044V131 View 3D Structure Click here
A0A044V263 View 3D Structure Click here
A0A044V4T9 View 3D Structure Click here
A0A044VIM1 View 3D Structure Click here
A0A077Z2I2 View 3D Structure Click here
A0A077Z4S1 View 3D Structure Click here
A0A077Z9J3 View 3D Structure Click here
A0A077ZAQ5 View 3D Structure Click here
A0A077ZBG2 View 3D Structure Click here
A0A077ZF26 View 3D Structure Click here
A0A0A2V1G0 View 3D Structure Click here
A0A0A2V2D6 View 3D Structure Click here
A0A0A2V3G0 View 3D Structure Click here
A0A0A2V3N5 View 3D Structure Click here
A0A0A2V3W7 View 3D Structure Click here
A0A0A2V4P9 View 3D Structure Click here
A0A0D2F839 View 3D Structure Click here
A0A0D2GCR0 View 3D Structure Click here
A0A0D2GMU4 View 3D Structure Click here
A0A0D2GNX7 View 3D Structure Click here
A0A0D2H3L4 View 3D Structure Click here
A0A0G2JXQ2 View 3D Structure Click here
A0A0G2JYP0 View 3D Structure Click here
A0A0G2JYS6 View 3D Structure Click here
A0A0G2K7D8 View 3D Structure Click here
A0A0G2KA92 View 3D Structure Click here
A0A0G2KYC1 View 3D Structure Click here
A0A0H5S869 View 3D Structure Click here
A0A0K0DRY2 View 3D Structure Click here
A0A0K0DS61 View 3D Structure Click here
A0A0K0DU01 View 3D Structure Click here
A0A0K0DV54 View 3D Structure Click here
A0A0K0DWF7 View 3D Structure Click here
A0A0K0DWX9 View 3D Structure Click here
A0A0K0DZ10 View 3D Structure Click here
A0A0K0DZQ1 View 3D Structure Click here