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60  structures 1452  species 0  interactions 4790  sequences 82  architectures

Family: CAF1C_H4-bd (PF12265)

Summary: Histone-binding protein RBBP4 or subunit C of CAF1 complex

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

Histone-binding protein RBBP4 or subunit C of CAF1 complex Provide feedback

The CAF-1 complex is a conserved heterotrimeric protein complex that promotes histone H3 and H4 deposition onto newly synthesized DNA during replication or DNA repair; specifically it facilitates replication-dependent nucleosome assembly with the major histone H3 (H3.1). This domain is an alpha helix which sits just upstream of the WD40 seven-bladed beta-propeller in the human RbAp46 protein. RbAp46 folds into the beta-propeller and binds histone H4 in a groove formed between this N-terminal helix and an extended loop inserted into blade six [1].

Literature references

  1. Murzina NV, Pei XY, Zhang W, Sparkes M, Vicente-Garcia J, Pratap JV, McLaughlin SH, Ben-Shahar TR, Verreault A, Luisi BF, Laue ED;, Structure. 2008;16:1077-1085.: Structural basis for the recognition of histone H4 by the histone-chaperone RbAp46. PUBMED:18571423 EPMC:18571423


This tab holds annotation information from the InterPro database.

InterPro entry IPR022052

This entry rerpesnts the N-terminal domain of the histone-binding protein RBBP4. Proteins containing this domain include members from the WD repeat RBAP46 (RBBP7)/RBAP48(RBBP4)/MSI1 family.

RBBP4 is a subunit of the chromatin assembly factor 1 (CAF-1) complex. The CAF-1 complex is a conserved heterotrimeric protein complex that promotes histone H3 and H4 deposition onto newly synthesized DNA during replication or DNA repair; specifically it facilitates replication-dependent nucleosome assembly with the major histone H3 (H3.1). This domain is an alpha helix which sits just upstream of the WD40 seven-bladed beta-propeller in the human RBBP7 protein. RBBP7 folds into the beta-propeller and binds histone H4 in a groove formed between this N-terminal helix and an extended loop inserted into blade six [ PUBMED:18571423 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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
(229)
Full
(4790)
Representative proteomes UniProt
(8020)
RP15
(854)
RP35
(2131)
RP55
(3682)
RP75
(4972)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(229)
Full
(4790)
Representative proteomes UniProt
(8020)
RP15
(854)
RP35
(2131)
RP55
(3682)
RP75
(4972)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(229)
Full
(4790)
Representative proteomes UniProt
(8020)
RP15
(854)
RP35
(2131)
RP55
(3682)
RP75
(4972)
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: Pfam-B_318 (release 23.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Wood V , Coggill P
Number in seed: 229
Number in full: 4790
Average length of the domain: 69.50 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 15.59 %

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 22.7 22.7
Trusted cut-off 22.7 22.9
Noise cut-off 22.5 22.6
Model length: 69
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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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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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 CAF1C_H4-bd domain has been found. There are 60 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
A0A0P0X2I9 View 3D Structure Click here
A0A0R0H7S6 View 3D Structure Click here
A0A1D6G362 View 3D Structure Click here
A0A1D6GLJ3 View 3D Structure Click here
A0A1D6KX72 View 3D Structure Click here
A0A1D6NE84 View 3D Structure Click here
A0A1D6NE96 View 3D Structure Click here
A0A1D6NQ77 View 3D Structure Click here
A0A1D8PFH2 View 3D Structure Click here
A0A1D8PRH3 View 3D Structure Click here
A0A2R8QUT0 View 3D Structure Click here
A4I5C6 View 3D Structure Click here
A4I953 View 3D Structure Click here
B4FLB4 View 3D Structure Click here
B4FZY9 View 3D Structure Click here
B5DFB2 View 3D Structure Click here
D4A250 View 3D Structure Click here
E9AH35 View 3D Structure Click here
F1QGP3 View 3D Structure Click here
I1K352 View 3D Structure Click here
I1K3M3 View 3D Structure Click here
I1KRH4 View 3D Structure Click here
I1KS25 View 3D Structure Click here
I1L1H2 View 3D Structure Click here
I1LIH2 View 3D Structure Click here
I1LPT2 View 3D Structure Click here
I1MH75 View 3D Structure Click here
O14021 View 3D Structure Click here
O22467 View 3D Structure Click here
O22468 View 3D Structure Click here
O22469 View 3D Structure Click here
O22607 View 3D Structure Click here
O94244 View 3D Structure Click here
P13712 View 3D Structure Click here
P39984 View 3D Structure Click here
P90916 View 3D Structure Click here
P90917 View 3D Structure Click here
Q04225 View 3D Structure Click here
Q09028 View 3D Structure Click here
Q10G81 View 3D Structure Click here
Q16576 View 3D Structure Click here
Q24572 View 3D Structure Click here
Q2RAX1 View 3D Structure Click here
Q4D4E9 View 3D Structure Click here
Q4DRW3 View 3D Structure Click here
Q4DXX2 View 3D Structure Click here
Q54ED4 View 3D Structure Click here
Q54SD4 View 3D Structure Click here
Q59RH5 View 3D Structure Click here
Q59ZD9 View 3D Structure Click here
Q5NAI9 View 3D Structure Click here
Q5XI13 View 3D Structure Click here
Q60972 View 3D Structure Click here
Q60973 View 3D Structure Click here
Q651E0 View 3D Structure Click here
Q6P3H7 View 3D Structure Click here
Q71UF4 View 3D Structure Click here
Q7ZTY4 View 3D Structure Click here
Q810D6 View 3D Structure Click here
Q8I238 View 3D Structure Click here
Q8IAZ7 View 3D Structure Click here
Q8IE52 View 3D Structure Click here
Q8ILD0 View 3D Structure Click here
Q8SYL1 View 3D Structure Click here
Q8W514 View 3D Structure Click here
Q9BQ67 View 3D Structure Click here
Q9N393 View 3D Structure Click here
Q9P783 View 3D Structure Click here
Q9SU78 View 3D Structure Click here
Q9Y825 View 3D Structure Click here
Q9ZUN8 View 3D Structure Click here