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24  structures 177  species 3  interactions 489  sequences 9  architectures

Family: Chromo_shadow (PF01393)

Summary: Chromo shadow domain

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Chromo shadow domain Edit Wikipedia article

Chromo shadow domain
PDB 1s4z EBI.jpg
hp1 chromo shadow domain in complex with pxvxl motif of caf-1
Identifiers
Symbol Chromo_shadow
Pfam PF01393
Pfam clan CL0049
InterPro IPR008251
SCOP 1e0b
SUPERFAMILY 1e0b
CDD cd00034

In molecular biology, the chromo shadow domain is a protein domain which is distantly related to the chromodomain. It is always found in association with a chromodomain. [1] Proteins containing a chromo shadow domain include Drosophila and human heterochromatin protein Su(var)205 (HP1); and mammalian modifier 1 and modifier 2.

Chromoshadow domains self aggregate, bringing together the nucleosomes to which their proteins are bound and thus condense the chromatin region they are associated with. Condensed chromatin is not able to be transcribed as the transcription factors and enzymes are not able to access to DNA sequence in this form. Hence chromoshadow domain containing proteins repress gene transcription.[2]

References[edit]

This article incorporates text from the public domain Pfam and InterPro IPR008251

External links[edit]

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 shadow domain Provide feedback

This domain is distantly related to PF00385. This domain is always found in association with a chromo domain.

Literature references

  1. Aasland R, Stewart AF; , Nucleic Acids Res 1995;23:3163-3173.: The chromo shadow domain, a second chromo domain in heterochromatin-binding protein 1, HP1. PUBMED:7667093 EPMC:7667093


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008251

Chromo shadow domain is distantly related to chromo domain. It is always found in association with a chromo domain.

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 [PUBMED:7667093], eg. Drosophila and human heterochromatin protein Su(var)205 (HP1); and mammalian modifier 1 and modifier 2. The second class includes proteins with a single chromo domain, eg. Drosophila protein Polycomb (Pc); mammalian modifier 3; human Mi-2 autoantigenand 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.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 14 members:

53-BP1_Tudor 7kD_DNA_binding Agenet Chromo Chromo_shadow DUF1325 DUF4537 MBT PWWP Rad9_Rad53_bind RBB1NT SMN TUDOR Tudor-knot

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...

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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.

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(8)
Full
(489)
Representative proteomes NCBI
(474)
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(69)
RP35
(99)
RP55
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RP75
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  Seed
(8)
Full
(489)
Representative proteomes NCBI
(474)
Meta
(0)
RP15
(69)
RP35
(99)
RP55
(194)
RP75
(286)
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
(8)
Full
(489)
Representative proteomes NCBI
(474)
Meta
(0)
RP15
(69)
RP35
(99)
RP55
(194)
RP75
(286)
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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.

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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: Medline:95396576
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 8
Number in full: 489
Average length of the domain: 56.80 aa
Average identity of full alignment: 49 %
Average coverage of the sequence by the domain: 28.14 %

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 20.8 20.8
Trusted cut-off 20.8 20.8
Noise cut-off 20.7 20.7
Model length: 58
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 3 interactions for this family. More...

ENT Chromo_shadow CAF-1_p150

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_shadow domain has been found. There are 24 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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