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0  structures 134  species 0  interactions 7406  sequences 24  architectures

Family: HCV_core (PF01542)

Summary: Hepatitis C virus core protein

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Hepatitis C virus core protein Provide feedback

The viral core protein forms the internal viral coat that encapsidates the genomic RNA and is enveloped in a host cell-derived lipid membrane. The core protein has been shown, by yeast two-hybrid assay to interact with cellular DEAD box helicases [1]. The N terminus of the core protein is involved in transcriptional repression [2].

Literature references

  1. Owsianka AM, Patel AH; , Virology 1999;257:330-340.: Hepatitis C virus core protein interacts with a human DEAD box protein DDX3. PUBMED:10329544 EPMC:10329544

  2. Ray RB, Ghosh AK, Meyer K, Ray R; , Virus Res 1999;59:211-217.: Functional analysis of a transrepressor domain in the hepatitis C virus core protein. PUBMED:10082392 EPMC:10082392


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002521

The Hepatitis C virus (HCV) is a small (50 nm in size), enveloped, single-stranded, positive sense RNA virus. It is the only known member of the hepacivirus genus in the family Flaviviridae. There are six major genotypes of the hepatitis C virus, which are identified numerically (e.g., genotype 1, genotype 2, etc.). Although Hepatitis A virus, Hepatitis B virus, and Hepatitis C virus have similar names, because they all cause liver inflammation, these are distinctly different viruses both genetically and clinically.

HCV has a positive sense RNA genome that consists of a single open reading frame of 9600 nucleotides. At the 5' and 3' ends of the RNA are the UTR regions that are not translated into proteins but are important to translation and replication of the viral RNA. The 5' UTR has a ribosome binding site (IRES - Internal ribosome entry site) that starts the translation of a 3000 amino acid containing protein that is later cut by cellular and viral proteases into 10 active structural and non-structural smaller proteins.

The HCV core protein is located at the N terminus of the polyprotein and is followed by the signal sequence located between the core protein and the E1 envelope glycoprotein. This signal sequence targets the nascent HCV polyprotein to the endoplasmic reticulum (ER), allowing the translocation of E1 to the ER lumen. Cleavage by a signal peptidase in the ER lumen releases the N-terminal end of E1, leaving the 191-amino acids (aa) core protein anchored by its C-terminal signal peptide [PUBMED:12145199, PUBMED:9621068]. This 191aa polypeptide, also known as p23, is the immature form of the core protein; p23 is further processed by an intramembrane protease, the signal peptide peptidase (SPP), that removes the ER anchor , releasing p21, the N-terminal 179aa mature form of the core protein [PUBMED:12145199]. Core protein (p21) is responsible for packaging viral RNA to form a viral nucleocapsid, and it also promotes virion budding [PUBMED:16528035].

Two domains have been identified in the mature form of the HCV core protein, based on predicted structural and functional characteristics [PUBMED:10900028]. Domain I, corresponding to the N-terminal region of approximately 120 aa, is a highly basic domain that is probably involved in the recruitment of viral RNA during particle morphogenesis. Domain II, located between aa 120 and aa 175, is a hydrophobic region predicted to form one or two alpha-helices that are probably involved in the association of core with the ER membrane and lipid droplets.

This entry represents domain II and domain III (ER anchor sequence) of the core protein p23.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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.

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(6)
Full
(7406)
Representative proteomes NCBI
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  Seed
(6)
Full
(7406)
Representative proteomes NCBI
(5245)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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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
(6)
Full
(7406)
Representative proteomes NCBI
(5245)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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: Swiss-Prot
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 6
Number in full: 7406
Average length of the domain: 59.90 aa
Average identity of full alignment: 89 %
Average coverage of the sequence by the domain: 8.38 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.6 21.6
Trusted cut-off 21.8 21.8
Noise cut-off 21.1 21.2
Model length: 75
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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