Summary: Influenza non-structural protein (NS1)
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This is the Wikipedia entry entitled "Influenza non-structural protein". More...
Influenza non-structural protein Edit Wikipedia article
Influenza non-structural protein (NS1) | |||||||||||
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Identifiers | |||||||||||
Symbol | Flu_NS1 | ||||||||||
Pfam | PF00600 | ||||||||||
InterPro | IPR000256 | ||||||||||
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Influenza non-structural protein (NS1) is a homodimeric RNA-binding protein found in influenza virus that is required for viral replication. NS1 binds polyA tails of mRNA keeping them in the nucleus. NS1 inhibits pre-mRNA splicing by tightly binding to a specific stem-bulge of U6 snRNA[1].
References
- ^ Huang Y, Rios CB, Tejero R, Zimmerman DE, Krug RM, Montelione GT, Chien CY (1997). "A novel RNA-binding motif in influenza A virus non-structural protein 1". Nat. Struct. Biol. 4 (11): 891–895. PMID 9360601.
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: CS1 maint: multiple names: authors list (link)
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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.
Influenza non-structural protein (NS1) Provide feedback
NS1 is a homodimeric RNA-binding protein that is required for viral replication. NS1 binds polyA tails of mRNA keeping them in the nucleus. NS1 inhibits pre-mRNA splicing by tightly binding to a specific stem-bulge of U6 snRNA.
Literature references
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Chien C, Tejero R, Huang Y, Zimmerman DE, Rios CB, Krug RM, Montelione GT; , Nat Struct Biol 1997;4:891-895.: A novel RNA-binding motif in influenza A virus non- structural protein 1. PUBMED:9360601 EPMC:9360601
External database links
SCOP: | 1ns1 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR000256
NS1 is a homodimeric RNA-binding protein found in influenza virus that is required for viral replication. NS1 binds polyA tails of mRNA keeping them in the nucleus. NS1 inhibits pre-mRNA splicing by tightly binding to a specific stem-bulge of U6 snRNA [ PUBMED:9360601 ].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | RNA binding (GO:0003723) |
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 S15_NS1 (CL0600), which has the following description:
The clan contains the following 4 members:
Flu_B_NS1 Flu_NS1 Ribosomal_S15 WHEP-TRSAlignments
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 (2) |
Full (25) |
Representative proteomes | UniProt (57219) |
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RP15 (30) |
RP35 (30) |
RP55 (30) |
RP75 (31) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (2) |
Full (25) |
Representative proteomes | UniProt (57219) |
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RP15 (30) |
RP35 (30) |
RP55 (30) |
RP75 (31) |
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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: | Bateman A |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Bateman A |
Number in seed: | 2 |
Number in full: | 25 |
Average length of the domain: | 217.1 aa |
Average identity of full alignment: | 82 % |
Average coverage of the sequence by the domain: | 95.23 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 217 | ||||||||||||
Family (HMM) version: | 22 | ||||||||||||
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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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 Flu_NS1 domain has been found. There are 125 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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