Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
209  structures 1470  species 0  interactions 26328  sequences 925  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

Chromodomain
PDB 1pfb EBI.jpg
Structure of polycomb chromodomain.[1]
Identifiers
SymbolChromodomain
PfamPF00385
InterProIPR000953
SMARTSM00298
PROSITEPS50013
SCOPe1pfb / SUPFAM
CDDcd00024

A chromodomain (chromatin organization modifier[2]) is a 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.[3] In mammals, chromodomain-containing proteins are responsible for aspects of gene regulation related to chromatin remodeling and formation of heterochromatin regions.[4] Chromodomain-containing proteins also bind methylated histones[5][6] and appear in the RNA-induced transcriptional silencing complex.[7]

See also

References

  1. ^ Min J, Zhang Y, Xu RM (August 2003). "Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27". Genes Dev. 17 (15): 1823–8. doi:10.1101/gad.269603. PMC 196225. PMID 12897052.
  2. ^ Messmer S, Franke A, Paro R (July 1992). "Analysis of the functional role of the Polycomb chromo domain in Drosophila melanogaster". Genes Dev. 6 (7): 1241–1254. doi:10.1101/gad.6.7.1241. PMID 1628830.
  3. ^ Tajul-Arifin K, Teasdale R, Ravasi T, Hume DA, Mattick JS (2003). "Identification and Analysis of Chromodomain-Containing Proteins Encoded in the Mouse Transcriptome". Genome Res. 13 (6B): 1416–1429. doi:10.1101/gr.1015703. PMC 403676. PMID 12819141.
  4. ^ Jones DO, Cowell IG, Singh PB (2000). "Mammalian chromodomain proteins: their role in genome organisation and expression". BioEssays. 22 (2): 124–37. CiteSeerX 10.1.1.575.6410. doi:10.1002/(SICI)1521-1878(200002)22:2<124::AID-BIES4>3.0.CO;2-E. PMID 10655032.
  5. ^ 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. doi:10.1038/nature722. PMID 11882902.
  6. ^ Jacobs SA, Khorasanizadeh S (2002). "Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail". Science. 295 (5562): 2080–3. doi:10.1126/science.1069473. PMID 11859155.
  7. ^ Verdel A, Jia S, Gerber S, Sugiyama T, Gygi S, Grewal SI, Moazed D (2004). "RNAi-Mediated Targeting of Heterochromatin by the RITS Complex". Science. 303 (5658): 672–6. doi:10.1126/science.1093686. PMC 3244756. PMID 14704433.

External links


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

No Pfam abstract.

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...

Loading domain graphics...

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

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 and the UniProtKB 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
(84)
Full
(26328)
Representative proteomes UniProt
(45496)
RP15
(4532)
RP35
(11971)
RP55
(21794)
RP75
(28793)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(84)
Full
(26328)
Representative proteomes UniProt
(45496)
RP15
(4532)
RP35
(11971)
RP55
(21794)
RP75
(28793)
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
(84)
Full
(26328)
Representative proteomes UniProt
(45496)
RP15
(4532)
RP35
(11971)
RP55
(21794)
RP75
(28793)
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.

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: Prosite
Previous IDs: chromo;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 84
Number in full: 26328
Average length of the domain: 54.50 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 6.61 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -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: 26
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 Chromo domain has been found. There are 209 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.

Loading structure mapping...

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
A0A0G2JXQ2 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
A0A0G2KA92 View 3D Structure Click here
A0A0G2KYC1 View 3D Structure Click here
A0A0P0VBB9 View 3D Structure Click here
A0A0P0VUY4 View 3D Structure Click here
A0A0R0FNY5 View 3D Structure Click here
A0A0R0FVG1 View 3D Structure Click here
A0A0R0HEG0 View 3D Structure Click here
A0A0R0IJ30 View 3D Structure Click here
A0A0R0IJ30 View 3D Structure Click here
A0A0R4IAE4 View 3D Structure Click here
A0A0R4IAE4 View 3D Structure Click here
A0A0R4IJ89 View 3D Structure Click here
A0A0R4IR86 View 3D Structure Click here
A0A0R4IR86 View 3D Structure Click here
A0A1D6EW42 View 3D Structure Click here
A0A1D6F350 View 3D Structure Click here
A0A1D6IBX9 View 3D Structure Click here
A0A1D6IMC7 View 3D Structure Click here
A0A1D6JMT9 View 3D Structure Click here
A0A1D6NTP5 View 3D Structure Click here
A0A1D6NTP5 View 3D Structure Click here
A0A1D8PCZ6 View 3D Structure Click here
A0A1D8PCZ6 View 3D Structure Click here
A0A1D8PTY4 View 3D Structure Click here
A0A2R8PZC6 View 3D Structure Click here
A0A2R8Q3B4 View 3D Structure Click here
A0A2R8Q3K5 View 3D Structure Click here
A0A2R8Q722 View 3D Structure Click here
A0A2R8Q7E1 View 3D Structure Click here
A0A2R8Q7F5 View 3D Structure Click here
A0A2R8Q9F9 View 3D Structure Click here
A0A2R8QA15 View 3D Structure Click here
A0A2R8QBY4 View 3D Structure Click here
A0A2R8QCU6 View 3D Structure Click here
A0A2R8QHS9 View 3D Structure Click here
A0A2R8QV54 View 3D Structure Click here
A0A2R8RNF4 View 3D Structure Click here
A0A2R8RP35 View 3D Structure Click here
A0A2R8RPI8 View 3D Structure Click here
A0A368UIJ7 View 3D Structure Click here
A0A368UK75 View 3D Structure Click here
A0A368UK75 View 3D Structure Click here
A1L223 View 3D Structure Click here
A1ZAW9 View 3D Structure Click here
A2A8L1 View 3D Structure Click here
A8KC45 View 3D Structure Click here
B0R0I6 View 3D Structure Click here
B0R0I6 View 3D Structure Click here
B0S768 View 3D Structure Click here
B1AR17 View 3D Structure Click here
B2RYU7 View 3D Structure Click here
B7ZUU4 View 3D Structure Click here
C0SQ89 View 3D Structure Click here
D3ZA12 View 3D Structure Click here
D3ZA12 View 3D Structure Click here
D3ZD32 View 3D Structure Click here
D3ZIH5 View 3D Structure Click here
D3ZRS6 View 3D Structure Click here
D4A3T3 View 3D Structure Click here
D4AAG9 View 3D Structure Click here
D4AAG9 View 3D Structure Click here
E7F6P0 View 3D Structure Click here
E7F7W5 View 3D Structure Click here
E7F7W5 View 3D Structure Click here
E7F8F2 View 3D Structure Click here
E9PT11 View 3D Structure Click here
E9PU01 View 3D Structure Click here
E9PZM4 View 3D Structure Click here
E9PZM4 View 3D Structure Click here
E9QDB7 View 3D Structure Click here
F1LPP8 View 3D Structure Click here
F1LT42 View 3D Structure Click here
F1Q982 View 3D Structure Click here
F1QM86 View 3D Structure Click here
F1QNF2 View 3D Structure Click here
F1QWV5 View 3D Structure Click here
F1RBK7 View 3D Structure Click here
F1RBT2 View 3D Structure Click here
F4IV99 View 3D Structure Click here
F4JTF6 View 3D Structure Click here
F4JTF6 View 3D Structure Click here
F4KBP5 View 3D Structure Click here
G3V6S6 View 3D Structure Click here
G3V8T1 View 3D Structure Click here
G5EBZ4 View 3D Structure Click here
G5EET5 View 3D Structure Click here
I1J8E3 View 3D Structure Click here
I1JMC3 View 3D Structure Click here
I1JPN1 View 3D Structure Click here
I1JSC2 View 3D Structure Click here
I1K6W8 View 3D Structure Click here
I1K8P5 View 3D Structure Click here
I1K8P5 View 3D Structure Click here
I1LIP2 View 3D Structure Click here
I1M733 View 3D Structure Click here
K7K149 View 3D Structure Click here
K7KED5 View 3D Structure Click here
K7KIF9 View 3D Structure Click here
K7KIF9 View 3D Structure Click here
K7KPZ4 View 3D Structure Click here
K7TNK0 View 3D Structure Click here
M0RAR7 View 3D Structure Click here
M0RE14 View 3D Structure Click here
O00257 View 3D Structure Click here
O14134 View 3D Structure Click here
O14139 View 3D Structure Click here
O14139 View 3D Structure Click here
O14646 View 3D Structure Click here
O14646 View 3D Structure Click here
O14647 View 3D Structure Click here
O14647 View 3D Structure Click here
O16102 View 3D Structure Click here
O16102 View 3D Structure Click here
O17909 View 3D Structure Click here
O17909 View 3D Structure Click here
O22265 View 3D Structure Click here
O42934 View 3D Structure Click here
O43463 View 3D Structure Click here
O49139 View 3D Structure Click here
O54864 View 3D Structure Click here
O55187 View 3D Structure Click here
O60016 View 3D Structure Click here
O95503 View 3D Structure Click here
O95931 View 3D Structure Click here
O97159 View 3D Structure Click here
O97159 View 3D Structure Click here
P05205 View 3D Structure Click here
P23198 View 3D Structure Click here
P26017 View 3D Structure Click here
P30658 View 3D Structure Click here
P32657 View 3D Structure Click here
P32657 View 3D Structure Click here
P34618 View 3D Structure Click here
P40201 View 3D Structure Click here
P40201 View 3D Structure Click here
P40381 View 3D Structure Click here
P45968 View 3D Structure Click here
P45973 View 3D Structure Click here
P45975 View 3D Structure Click here
P60889 View 3D Structure Click here
P83916 View 3D Structure Click here
P83917 View 3D Structure Click here
Q08972 View 3D Structure Click here
Q09XV5 View 3D Structure Click here
Q09XV5 View 3D Structure Click here
Q0JAE0 View 3D Structure Click here
Q10103 View 3D Structure Click here
Q12873 View 3D Structure Click here
Q13185 View 3D Structure Click here
Q14781 View 3D Structure Click here
Q14839 View 3D Structure Click here
Q18313 View 3D Structure Click here
Q19972 View 3D Structure Click here
Q19973 View 3D Structure Click here
Q22430 View 3D Structure Click here
Q22516 View 3D Structure Click here
Q339W7 View 3D Structure Click here
Q3TYA6 View 3D Structure Click here
Q4FZS1 View 3D Structure Click here
Q54AP9 View 3D Structure Click here
Q54Q16 View 3D Structure Click here
Q54Q16 View 3D Structure Click here
Q54RN0 View 3D Structure Click here
Q54RQ4 View 3D Structure Click here
Q54UZ8 View 3D Structure Click here
Q55C69 View 3D Structure Click here
Q55FF5 View 3D Structure Click here
Q5KQL9 View 3D Structure Click here
Q5RJK5 View 3D Structure Click here
Q61686 View 3D Structure Click here
Q6AYK9 View 3D Structure Click here
Q6AZW3 View 3D Structure Click here
Q6DGD3 View 3D Structure Click here
Q6IQ71 View 3D Structure Click here
Q6PDQ2 View 3D Structure Click here
Q6TH37 View 3D Structure Click here
Q7JXA8 View 3D Structure Click here
Q7KU24 View 3D Structure Click here
Q7KU24 View 3D Structure Click here
Q86BS3 View 3D Structure Click here
Q8I5K4 View 3D Structure Click here
Q8IHV8 View 3D Structure Click here
Q8LK11 View 3D Structure Click here
Q8LPU5 View 3D Structure Click here
Q8LSQ2 View 3D Structure Click here
Q8N8U2 View 3D Structure Click here
Q8TDI0 View 3D Structure Click here
Q8VDS3 View 3D Structure Click here
Q946J8 View 3D Structure Click here
Q94F87 View 3D Structure Click here
Q94F88 View 3D Structure Click here
Q99549 View 3D Structure Click here
Q9ARI6 View 3D Structure Click here
Q9AXT8 View 3D Structure Click here
Q9D5D8 View 3D Structure Click here
Q9DBY5 View 3D Structure Click here
Q9EQQ0 View 3D Structure Click here
Q9H5I1 View 3D Structure Click here
Q9HC52 View 3D Structure Click here
Q9HCK8 View 3D Structure Click here
Q9HCK8 View 3D Structure Click here
Q9JIX5 View 3D Structure Click here
Q9JIX5 View 3D Structure Click here
Q9QXV1 View 3D Structure Click here
Q9S775 View 3D Structure Click here
Q9S775 View 3D Structure Click here
Q9U3C6 View 3D Structure Click here
Q9US25 View 3D Structure Click here
Q9US25 View 3D Structure Click here
Q9VCU6 View 3D Structure Click here
Q9VHG0 View 3D Structure Click here
Q9VX35 View 3D Structure Click here
Q9W396 View 3D Structure Click here
Q9WTK2 View 3D Structure Click here
Q9Y232 View 3D Structure Click here
Q9Y6F7 View 3D Structure Click here
Q9Y6F8 View 3D Structure Click here
X1WBY5 View 3D Structure Click here