Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
694  structures 194  species 0  interactions 1876  sequences 16  architectures

Family: RnaseA (PF00074)

Summary: Pancreatic ribonuclease

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 "Pancreatic ribonuclease". More...

Pancreatic ribonuclease Edit Wikipedia article

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.

Pancreatic ribonuclease Provide feedback

Ribonucleases. Members include pancreatic RNAase A and angiogenins. Structure is an alpha+beta fold -- long curved beta sheet and three helices.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR023412

Pancreatic ribonucleases (RNaseA) are pyrimidine-specific endonucleases found in high quantity in the pancreas of certain mammals and of some reptiles [ PUBMED:3940901 ]. Specifically, the enzymes are involved in endonucleolytic cleavage of 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates. Ribonuclease can unwind the DNA helix by complexing with single-stranded DNA; the complex arises by an extended multi-site cation-anion interaction between lysine and arginine residues of the enzyme and phosphate groups of the nucleotides. Other proteins belonging to the pancreatic RNAse family include: bovine seminal vesicle and brain ribonucleases; kidney non-secretory ribonucleases [ PUBMED:2734298 ]; liver-type ribonucleases [ PUBMED:2611266 ]; angiogenin, which induces vascularisation of normal and malignant tissues; eosinophil cationic protein [ PUBMED:2473157 ], a cytotoxin and helminthotoxin with ribonuclease activity; and frog liver ribonuclease and frog sialic acid-binding lectin. The sequence of pancreatic RNases contains four conserved disulphide bonds and three amino acid residues involved in the catalytic activity.

This entry represents a domain in Ribonuclease A. Its structure is an alpha+beta fold -- long curved beta sheet and three helices.

Domain organisation

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

Loading domain graphics...

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
(140)
Full
(1876)
Representative proteomes UniProt
(3082)
RP15
(129)
RP35
(458)
RP55
(1262)
RP75
(1863)
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
(140)
Full
(1876)
Representative proteomes UniProt
(3082)
RP15
(129)
RP35
(458)
RP55
(1262)
RP75
(1863)
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
(140)
Full
(1876)
Representative proteomes UniProt
(3082)
RP15
(129)
RP35
(458)
RP55
(1262)
RP75
(1863)
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: Overington and HMM_iterative_training
Previous IDs: rnaseA;
Type: Domain
Sequence Ontology: SO:0000417
Author: Eddy SR
Number in seed: 140
Number in full: 1876
Average length of the domain: 114.1 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 69.8 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.1 23.1
Trusted cut-off 23.1 23.2
Noise cut-off 22.9 23.0
Model length: 121
Family (HMM) version: 23
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 RnaseA domain has been found. There are 694 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.

Loading structure mapping...

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
A5HAK0 View 3D Structure Click here
A5HAK1 View 3D Structure Click here
A5HAK2 View 3D Structure Click here
D4ABQ0 View 3D Structure Click here
E9PTM0 View 3D Structure Click here
E9PU07 View 3D Structure Click here
F6YUX7 View 3D Structure Click here
O35290 View 3D Structure Click here
O35291 View 3D Structure Click here
O35292 View 3D Structure Click here
O46525 View 3D Structure Click here
O46532 View 3D Structure Click here
O46533 View 3D Structure Click here
O55004 View 3D Structure Click here
P00669 View 3D Structure Click here
P00671 View 3D Structure Click here
P00674 View 3D Structure Click here
P00678 View 3D Structure Click here
P00679 View 3D Structure Click here
P00682 View 3D Structure Click here
P00683 View 3D Structure Click here
P00684 View 3D Structure Click here
P03950 View 3D Structure Click here
P07998 View 3D Structure Click here
P08904 View 3D Structure Click here
P10152 View 3D Structure Click here
P10153 View 3D Structure Click here
P12724 View 3D Structure Click here
P15467 View 3D Structure Click here
P15468 View 3D Structure Click here
P21570 View 3D Structure Click here
P27043 View 3D Structure Click here
P30374 View 3D Structure Click here
P31346 View 3D Structure Click here
P31347 View 3D Structure Click here
P34096 View 3D Structure Click here
P39873 View 3D Structure Click here
P47778 View 3D Structure Click here
P47779 View 3D Structure Click here
P47780 View 3D Structure Click here