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16  structures 157  species 1  interaction 366  sequences 10  architectures

Family: RB_A (PF01858)

Summary: Retinoblastoma-associated protein A domain

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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.

Retinoblastoma-associated protein A domain Provide feedback

This domain has the cyclin fold [1] as predicted [2].

Literature references

  1. Gibson TJ, Thompson JD, Blocker A, Kouzarides T; , Nucleic Acids Res 1994;22:946-952.: Evidence for a protein domain superfamily shared by the cyclins, TFIIB and RB/p107. PUBMED:8152925 EPMC:8152925

  2. Lee JO, Russo AA, Pavletich NP; , Nature 1998;391:859-865.: Structure of the retinoblastoma tumour-suppressor pocket domain bound to a peptide from HPV E7. PUBMED:9495340 EPMC:9495340


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002720

Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation. They form a complex with adenovirus E1A and Simian virus 40 (SV40) large T antigen, and may bind and modulate the function of certain cellular proteins with which T and E1A compete for pocket binding. The proteins may act as tumor suppressors, and are potent inhibitors of E2F-mediated trans-activation. This domain has the cyclin fold [PUBMED:8152925].

The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B-box portion of the pocket; the A-box portion appears to be required for the stable folding of the B box (see INTERPRO). Also highly conserved is the extensive A-B interface, suggesting that it may be an additional protein-binding site. The A and B boxes each contain the cyclin-fold structural motif, with the LxCxE-binding site on the B-box cyclin fold being similar to a Cdk2-binding site of cyclin A and to a TBP-binding site of TFIIB [PUBMED:9495340].

The A and B boxes are found at the C-terminal end of the protein; the A-box is on N-terminal side of the B-box.

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 Cyclin (CL0065), which has the following description:

This Clan contains cyclins, Transcription factor IIB (TFIIB), and the Retinoblastoma tumour suppressor proteins. These were predicted to be related by sequence [1].

The clan contains the following 7 members:

CDK5_activator Cyclin Cyclin_C Cyclin_N RB_A RB_B TFIIB

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...

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
(7)
Full
(366)
Representative proteomes NCBI
(368)
Meta
(1)
RP15
(49)
RP35
(77)
RP55
(127)
RP75
(185)
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PP/heatmap 1 View  View  View  View  View     
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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
(7)
Full
(366)
Representative proteomes NCBI
(368)
Meta
(1)
RP15
(49)
RP35
(77)
RP55
(127)
RP75
(185)
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
(7)
Full
(366)
Representative proteomes NCBI
(368)
Meta
(1)
RP15
(49)
RP35
(77)
RP55
(127)
RP75
(185)
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.

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.

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: Swiss-Prot
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 7
Number in full: 366
Average length of the domain: 188.10 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 21.11 %

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 25.0 25.0
Trusted cut-off 25.5 26.7
Noise cut-off 24.4 24.2
Model length: 194
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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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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Interactions

There is 1 interaction for this family. More...

RB_B

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 RB_A domain has been found. There are 16 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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