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2  structures 201  species 0  interactions 217  sequences 8  architectures

Family: Chromo_2 (PF18704)

Summary: Chromatin organization modifier domain 2

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This is the Wikipedia entry entitled "Chromodomain". More...

Chromodomain Edit Wikipedia article

Chromodomain
PDB 1pfb EBI.jpg
Structure of polycomb chromodomain.[1]
Identifiers
Symbol Chromodomain
Pfam PF00385
InterPro IPR000953
SMART SM00298
PROSITE PS50013
SCOP 1pfb
SUPERFAMILY 1pfb
CDD cd00024

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 196225Freely accessible. 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 403676Freely accessible. 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. 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 3244756Freely accessible. 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.

Chromatin organization modifier domain 2 Provide feedback

Chromodomains serve as chromatin-targeting modules, general protein interaction elements as well as dimerization sites. They are found in many chromatin-associated proteins that bind modified histone tails for chromatin targeting. Chromodomains often recognize modified lysines through their aromatic cage thus targeting proteins to chromatin. Family members such as GEN1 carry a chomodomain which directly contacts DNA and its truncation severely hampers GEN1's catalytic activity. The chromodomain allows GEN1 to correctly position itself against DNA molecules, and without the chromodomain, GEN1's ability to cut DNA was severely impaired. The GEN1 chromodomain was found to be distantly related to the CDY chromodomains and chromobox proteins, particularly to the chromo-shadow domains of CBX1, CBX3 and CBX5. Furthermore, it is conserved from yeast (Yen1) to humans with the only exception being the Caenorhabditis elegans GEN1, which has a much smaller protein size of 443 amino acids compared to yeast Yen1 (759 aa) or human GEN1 (908 aa) [1].

Literature references

  1. Lee SH, Princz LN, Klugel MF, Habermann B, Pfander B, Biertumpfel C;, Elife. 2015; [Epub ahead of print]: Human Holliday junction resolvase GEN1 uses a chromodomain for efficient DNA recognition and cleavage. PUBMED:26682650 EPMC:26682650


Internal database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

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

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...

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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.

  Seed
(53)
Full
(217)
Representative proteomes UniProt
(302)
NCBI
(609)
Meta
(0)
RP15
(46)
RP35
(94)
RP55
(175)
RP75
(210)
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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
(53)
Full
(217)
Representative proteomes UniProt
(302)
NCBI
(609)
Meta
(0)
RP15
(46)
RP35
(94)
RP55
(175)
RP75
(210)
Alignment:
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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
(53)
Full
(217)
Representative proteomes UniProt
(302)
NCBI
(609)
Meta
(0)
RP15
(46)
RP35
(94)
RP55
(175)
RP75
(210)
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.

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

This family is new in this Pfam release.

Seed source: ECOD:EUF07587
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: El-Gebali S
Number in seed: 53
Number in full: 217
Average length of the domain: 65.00 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 9.03 %

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 25.0 25.0
Trusted cut-off 25.9 25.5
Noise cut-off 24.7 24.9
Model length: 68
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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

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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 Chromo_2 domain has been found. There are 2 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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