Summary: Retinoblastoma-associated protein A domain
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Retinoblastoma-associated protein A domain Provide feedback
This domain has the cyclin fold [1] as predicted [2].
Literature references
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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
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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
SCOP: | 1gux |
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.
Cellular component | nucleus (GO:0005634) |
Biological process | regulation of cell cycle (GO:0051726) |
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 12 members:
CDK5_activator Cyclin Cyclin_C Cyclin_C_2 Cyclin_N DUF3452 Herp-Cyclin K-cyclin_vir_C RB_A RB_B TFIIB TFIIB_C_1Alignments
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 (66) |
Full (1424) |
Representative proteomes | UniProt (2312) |
NCBI (3592) |
Meta (1) |
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RP15 (188) |
RP35 (569) |
RP55 (1086) |
RP75 (1471) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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not generated,
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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 (66) |
Full (1424) |
Representative proteomes | UniProt (2312) |
NCBI (3592) |
Meta (1) |
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RP15 (188) |
RP35 (569) |
RP55 (1086) |
RP75 (1471) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Swiss-Prot |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 66 |
Number in full: | 1424 |
Average length of the domain: | 188.10 aa |
Average identity of full alignment: | 40 % |
Average coverage of the sequence by the domain: | 20.58 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 197 | ||||||||||||
Family (HMM) version: | 18 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
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 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 sequence.
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