Hepatitis C virus core protein, N-terminal (IPR002522)

Short name: HCV_core_N

Overlapping homologous superfamilies


Domain relationships



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 [PMID: 12145199, PMID: 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 [PMID: 12145199]. Core protein (p21) is responsible for packaging viral RNA to form a viral nucleocapsid, and it also promotes virion budding [PMID: 16528035].

Two domains have been identified in the mature form of the HCV core protein, based on predicted structural and functional characteristics [PMID: 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 covers domain I of the core protein.

GO terms

Biological Process

No terms assigned in this category.

Molecular Function

GO:0005198 structural molecule activity

Cellular Component

GO:0019028 viral capsid

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.