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1676  structures 1119  species 15  interactions 16563  sequences 217  architectures

Family: Histone (PF00125)

Summary: Core histone H2A/H2B/H3/H4

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 "Histone". More...

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.

Core histone H2A/H2B/H3/H4 Provide feedback

No Pfam abstract.

Literature references

  1. Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ; , Nature 1997;389:251-260.: Crystal structure of the nucleosome core particle at 2.8 A resolution. PUBMED:9305837 EPMC:9305837


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007125

Five major families of histones exist: H1/H5, H2A, H2B, H3, and H4 [PUBMED:16472024] Histones H2A, H2B, H3 and H4 are known as the core histones, while histones H1 and H5 are known as the linker histones. The core histones together with some other DNA binding proteins form a superfamily defined by a common fold and distant sequence similarities [PUBMED:7651829, PUBMED:9016552]. Some proteins contain local homology domains related to the histone fold [PUBMED:9305837].

This entry represents a domain found in histones H2A, H2B and H3.

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 Histone (CL0012), which has the following description:

Members of this clan all possess a histone fold. Generally proteins in this clan are DNA binding.

The clan contains the following 17 members:

Bromo_TP Bromo_TP_like CBFD_NFYB_HMF CENP-S CENP-T_C CENP-W CENP-X DUF1931 Histone PAF TAF TAF4 TAFII28 TFIID-18kDa TFIID-31kDa TFIID_20kDa TFIID_30kDa

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...

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
(29)
Full
(16563)
Representative proteomes UniProt
(51908)
NCBI
(35788)
Meta
(142)
RP15
(5120)
RP35
(9905)
RP55
(13925)
RP75
(16543)
Jalview View  View  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
(29)
Full
(16563)
Representative proteomes UniProt
(51908)
NCBI
(35788)
Meta
(142)
RP15
(5120)
RP35
(9905)
RP55
(13925)
RP75
(16543)
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
(29)
Full
(16563)
Representative proteomes UniProt
(51908)
NCBI
(35788)
Meta
(142)
RP15
(5120)
RP35
(9905)
RP55
(13925)
RP75
(16543)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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

Seed source: Prosite
Previous IDs: histone;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Sonnhammer ELL
Number in seed: 29
Number in full: 16563
Average length of the domain: 104.50 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 57.78 %

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 26.4 26.4
Trusted cut-off 26.4 26.4
Noise cut-off 26.3 26.3
Model length: 131
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

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

Selections

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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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Tree controls

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Interactions

There are 15 interactions for this family. More...

CAF1C_H4-bd PH CHZ RhoGEF SIR2 Daxx Histone Daxx Scm3 Scm3 ASF1_hist_chap SET BAH MHC_I WD40

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 Histone domain has been found. There are 1676 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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