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0  structures 78  species 0  interactions 111  sequences 27  architectures

Family: CoV_NSP3_C (PF19218)

Summary: Coronavirus replicase NSP3, C-terminal

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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.

Coronavirus replicase NSP3, C-terminal Provide feedback

This family represents the C-terminal region of non-structural protein NSP3 (also known as nsp3). NSP3 is the product of ORF1a. It is found in human SARS coronavirus polyprotein 1a and 1ab, and in related coronavirus polyproteins. It is a multifunctional protein comprising up to 16 different domains and regions. NSP3 binds to viral RNA, nucleocapsid protein, as well as other viral proteins and participates in polyprotein processing [1].

Literature references

  1. 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


This tab holds annotation information from the InterPro database.

InterPro entry IPR043611

Non-structural protein NSP3 (also known as nsp3) is a multi-domain protein, the largest product of ORF1a which encodes the poyprotein 1a/1ab (pp1a/1ab). NSP3 comprises up to 16 different domains and regions, their organisation differs between coronaviruses (CoV). However, eight domains and two transmembrane regions are conserved in all known CoVs: the ubiquitin-like domain 1 (Ubl1), the Glu-rich acidic domain (hypervariable region), a macrodomain (X domain), the ubiquitin-like domain 2 (Ubl2), the papain-like protease 2 (PL2pro, depending on the CoV there are one or two PLpro), the NSP3 ectodomain (3Ecto, also called "zinc-finger domain"), as well as the domains Y1 and CoV-Y of unknown function. NSP3 is released from pp1a/1ab by the papain-like protease domain(s), which is (are) part of NSP3 itself. NSP3 is an essential component of the replication/transcription complex (RTC) as it acts as a scaffold protein to interact with itself and to bind other viral NSPs or host proteins. The RTC associates with host ER membranes producing convoluted membranes and double-membrane vesicles. It is also involved in post-translational modifications of host proteins to antagonise its innate immune response [ PUBMED:29162711 , PUBMED:29128390 ].

This entry represents the C-terminal region of NSP3 found in coronaviruses.

Domain organisation

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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
(23)
Full
(111)
Representative proteomes UniProt
(14046)
RP15
(117)
RP35
(117)
RP55
(117)
RP75
(117)
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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
(23)
Full
(111)
Representative proteomes UniProt
(14046)
RP15
(117)
RP35
(117)
RP55
(117)
RP75
(117)
Alignment:
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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
(23)
Full
(111)
Representative proteomes UniProt
(14046)
RP15
(117)
RP35
(117)
RP55
(117)
RP75
(117)
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: Mannual
Previous IDs: Corona_NSP3_C;
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Chuguransky S
Number in seed: 23
Number in full: 111
Average length of the domain: 473.30 aa
Average identity of full alignment: 34 %
Average coverage of the sequence by the domain: 8.08 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 288.8 288.8
Noise cut-off 20.1 19.7
Model length: 459
Family (HMM) version: 2
Download: download the raw HMM for this family

Species distribution

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