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3  structures 944  species 0  interactions 1163  sequences 22  architectures

Family: Nop53 (PF07767)

Summary: Nop53 (60S ribosomal biogenesis)

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.

Nop53 (60S ribosomal biogenesis) Provide feedback

This nucleolar family of proteins are involved in 60S ribosomal biogenesis. They are specifically involved in the processing beyond the 27S stage of 25S rRNA maturation [3]. This family contains sequences that bear similarity to the glioma tumour suppressor candidate region gene 2 protein (p60) [1]. This protein has been found to interact with herpes simplex type 1 regulatory proteins [1].

Literature references

  1. Smith JS, Tachibana I, Pohl U, Lee HK, Thanarajasingam U, Portier BP, Ueki K, Ramaswamy S, Billings SJ, Mohrenweiser HW, Louis DN, Jenkins RB; , Genomics 2000;64:44-50.: A transcript map of the chromosome 19q-arm glioma tumor suppressor region. PUBMED:10708517 EPMC:10708517

  2. Bruni R, Fineschi B, Ogle WO, Roizman B; , J Virol 1999;73:3810-3817.: A novel cellular protein, p60, interacting with both herpes simplex virus 1 regulatory proteins ICP22 and ICP0 is modified in a cell-type-specific manner and Is recruited to the nucleus after infection. PUBMED:10196275 EPMC:10196275

  3. Sydorskyy Y, Dilworth DJ, Halloran BP, Yi EC, Makhnevych TR, Wozniak RW, Aitchison JD; , Biochem J 2005; [Epub ahead of print]: Nop53p is a novel nucleolar 60S ribosomal biogenesis protein. PUBMED:15686447 EPMC:15686447


This tab holds annotation information from the InterPro database.

InterPro entry IPR011687

This entry includes glioma tumour suppressor candidate region gene 2 protein (GSCR2) from humans and ribosome biogenesis protein Nop53 from budding yeasts. GSCR2 bears similarity to the glioma tumour suppressor candidate region gene 2 protein (p60) [PUBMED:10708517]. Nop53 is a nucleolar protein that is involved in biogenesis of the 60S subunit of the ribosome [PUBMED:15686447]. It interacts with Nop17 and Nip7 and is required for pre-rRNA processing in Saccharomyces cerevisiae [PUBMED:16128814].

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, 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
(142)
Full
(1163)
Representative proteomes UniProt
(1728)
NCBI
(1912)
Meta
(2)
RP15
(341)
RP35
(673)
RP55
(923)
RP75
(1120)
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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
(142)
Full
(1163)
Representative proteomes UniProt
(1728)
NCBI
(1912)
Meta
(2)
RP15
(341)
RP35
(673)
RP55
(923)
RP75
(1120)
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
(142)
Full
(1163)
Representative proteomes UniProt
(1728)
NCBI
(1912)
Meta
(2)
RP15
(341)
RP35
(673)
RP55
(923)
RP75
(1120)
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: Pfam-B_8778 (release 14.0)
Previous IDs: P60;
Type: Family
Sequence Ontology: SO:0100021
Author: Fenech M , Wood V , Mistry J
Number in seed: 142
Number in full: 1163
Average length of the domain: 329.20 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 82.94 %

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 24.9 24.9
Trusted cut-off 25.2 25.0
Noise cut-off 24.4 24.7
Model length: 398
Family (HMM) version: 11
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 Nop53 domain has been found. There are 3 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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