Summary: Betacoronavirus nucleic acid-binding (NAR)
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Betacoronavirus nucleic acid-binding (NAR) Provide feedback
This domain, approximately 100 residues in length, is found in the multidomain nonstructural protein NSP3, and described as NSP3e domain. NSP3 is part of Orf1a polyproteins in SARS-CoV [1]. It is an essential component of the replication/transcription complex [2]. The global domain of the NAR represents a new fold, with a parallel four-strand beta-sheet holding two alpha-helices of three and four turns that are oriented antiparallel to the beta-strands and a group of residues form a positively charged patch on the protein surface as the binding site responsible for binding affinity for nucleic acids. When binding to ssRNA, the NAR prefers sequences with repeats of three consecutive Gs, such as (GGGA)5 and (GGGA)2. A positively charged surface patch (Lys75, Lys76, Lys99, and Arg106) is involved in RNA binding [2, 3].
Literature references
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Rota PA, Oberste MS, Monroe SS, Nix WA, Campagnoli R, Icenogle JP, Peñaranda S, Bankamp B, Maher K, Chen MH, Tong S, Tamin A, Lowe L, Frace M, DeRisi JL, Chen Q, Wang D, Erdman DD, Peret TC, Burns C, Ksiazek TG, Rollin PE, Sanchez A, Liffick S, Holloway B, Limor J, McCaustland K, Olsen-Rasmussen M, Fouchier R, Günther S, Osterhaus AD, Drosten C, Pallansch MA, Anderson LJ, Bellini WJ., Science 300 (5624), 1394-1399 (2003): Characterization of a novel coronavirus associated with severe acute respiratory syndrome PUBMED:12730500 EPMC:12730500
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Lei J, Kusov Y, Hilgenfeld R;, Antiviral Res. 2018;149:58-74.: Nsp3 of coronaviruses: Structures and functions of a large multi-domain protein. PUBMED:29128390 EPMC:29128390
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Serrano P, Johnson MA, Chatterjee A, Neuman BW, Joseph JS, Buchmeier MJ, Kuhn P, Wüthrich K., J. Virol. 83 (24), 12998-13008 (2009).: Nuclear magnetic resonance structure of the nucleic acid-binding domain of severe acute respiratory syndrome coronavirus nonstructural protein 3. PUBMED:19828617 EPMC:19828617
This tab holds annotation information from the InterPro database.
InterPro entry IPR032592
This domain, approximately 100 residues in length, is mainly found in Orf1a polyproteins in severe acute respiratory syndrome coronavirus [PUBMED:12730500]. The global domain of the NAR represents a new fold, with a parallel four-strand beta-sheet holding two alpha-helices of three and four turns that are oriented antiparallel to the beta-strands and a group of residues form a positively charged patch on the protein surface as the binding site responsible for binding affinity for nucleic acids [PUBMED:19828617].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | nucleic acid binding (GO:0003676) |
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
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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 (2) |
Full (51) |
Representative proteomes | UniProt (1409) |
NCBI (1408) |
Meta (0) |
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RP15 (51) |
RP35 (51) |
RP55 (51) |
RP75 (51) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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Seed (2) |
Full (51) |
Representative proteomes | UniProt (1409) |
NCBI (1408) |
Meta (0) |
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RP15 (51) |
RP35 (51) |
RP55 (51) |
RP75 (51) |
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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: | Jackhmmer JCSG taget SARS168 and PDB 2K87 |
Previous IDs: | NAR; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Chang Y |
Number in seed: | 2 |
Number in full: | 51 |
Average length of the domain: | 116.60 aa |
Average identity of full alignment: | 44 % |
Average coverage of the sequence by the domain: | 1.98 % |
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: | 117 | ||||||||||||
Family (HMM) version: | 6 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 bCoV_NAR domain has been found. There are 1 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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