Structure Details

The initial cleavage of the core by a host signal peptidase generates an immature core protein that is 191 amino acids long. A second cleavage by a signal peptide peptidase removes the C-terminal E1 signal sequence, releasing the mature core protein that is 177 amino acids long and 21-kDa in weight. The mature core protein is composed of two distinct domains: D1 (at the N-terminal region) and D2 (at the C-terminal region). The D1 domain is highly flexible in structure and subdivided into three basic domains (BD): BD1, BD2, and BD3. During assembly, the D1 domain is involved in RNA binding and oligomerization (around the RNA scaffolding) to form the nucleocapsid. The D2 domain contains the Helix I and Helix II regions, which are connected by a hydrophobic loop, and contributes to interactions with lipid membranes. The D3 domain corresponds to the extreme C-terminal region that is cleaved and therefore is absent in the mature capsid protein.

Structure Details

E1 is a type I transmembrane protein that has a molecular weight of 23 kDa and is 192 amino acids long. The E1 protein has four main domains: an N-terminal domain (NTD), a putative fusion peptide (pFP), a conserved region (CR), and a short C-terminal transmembrane domain (TMD). The E1 protein contains 4-5 N-linked glycans. On the surface of HCV, most of the E1 immunogenic domains are hidden below E2 in the E1-E2 heterodimer, which explains why the E1 proteins are considered significantly less immunogenic than E2 proteins. The E1 highly conserved GxxxG motif (Gly354 and Gly358), which is located in the transmembrane domain plays an essential role in the formation of the E1 trimer. In addition, the CxxC motif (Cys 226 and Cys 229), appears to play a role during virus entry.

Structure Details

The E2 protein has a molecular weight of 70 kDa and is 363 amino acids long. The E2 protein contains hypervariable region 1 (HVR1), HVR2, intergenotypic variable region (igVR), a stem region, and a transmembrane (TM) domain. The E2 protein undergoes N-linked glycosylation at 9 to 11 sites and has 18 conserved cysteine residues; this process is important for proper protein folding and immune evasion. The heavily glycosylated regions on E2 contain immunodominant neutralization epitopes that are believed to function as immunological decoys to shield more conserved neutralization epitopes. Although genetic heterogeneity can be found throughout the HCV genome, the N-terminus of the E2 glycoprotein can be highly variable and change rapidly even within a patient.

Structure Details

The p7 protein has a molecular weight of only 7 kDa and is only 63 amino acids long. The protein consists of an N-terminal region, transmembrane domain 1 (TM1), a short loop, transmembrane domain 2 (TM2), and a C-terminal end. The N-terminal and C-terminal regions of p7 are both oriented toward the endoplasmic reticulum lumen, whereas the short, intervening loop extends into the cytoplasm. The TM1 and TM2 domains are alpha helixes. The p7 oligomers have been identified in heptameric and hexameric forms. 

Structure Details

The dimeric NS2 protein has a molecular weight of 21 kDa and is 217 amino acids long. NS2 has three transmembrane domains, a small alpha helix, and a protease domain (that faces the cytosol). The NS2 protein has two active sites and functions as a cysteine protease, with its C-terminal domain (cleaving the NS2-NS3 junction in coordination with the N-terminal 180 amino acids of the NS3 protein. The protease domain forms a dimer that consists of an N-terminal alpha-helical subdomain and a domain-swapped C-terminal antiparallel beta sheet. The protease domain houses catalytic activity in the C-terminal at the catalytic triad: His 143, Glu 163, and Cys 184. The N-terminal transmembrane segment of NS2 is the region thought to play a central role in HCV particle assembly.

Structure Details

The NS3 protein has a molecular weight of 70kDa and is 631 amino acids long. The protein has two major domains: (1) the serine protease domain in N-terminal region (180 amino acids long) and (2) the larger nucleoside-triphosphatase-dependent RNA helicase domain in the C-terminal region that is 450 amino acids long. The N-terminal domain contains the protease catalytic triad at highly conserved amino acid positions (Histidine-57, Aspartate-81, and Serine-139); the serine protease is stabilized by a Zn²⁺ atom. At the membrane, the NS3 protein is anchored by the 54-amino-acid NS4 protein and together they form the NS3-4A enzyme complex.

Structure Details

The NS4A protein is the smallest of the nonstructural HCV proteins—it is 27 kDa in weight and is 54 amino acids in length. The NS4A protein has three domains: (1) N-terminal hydrophobic portion that forms a transmembrane alpha-helix essential for the integral membrane association of the NS3-4A complex, (2) a central region that is required for proper folding of NS3, and (3) a C-terminal acidic portion that comprises a highly negatively charged α-helix involved in regulating NS5A hyperphosphorylation and viral replication.

Structure Details

The hydrophobic NS4B protein is 27kDa in size and 261 amino acids long. This hydrophobic protein has a complex structure consisting of an N-terminal helix in the endoplasmic reticulum lumen, a central region consisting of four-five transmembrane segments, and a C-terminal region in the cytosolic lumen that contains several helices. Prior to proteolytic cleavage, the NS4B is attached to NS4A, with both N-terminal and C-terminal components located in the cytosolic lumen (flanking four transmembrane NS4B segments). Following the NS34A cleavage of the NS4A and NS4B, the N-terminal region flips into the endoplasmic reticulum lumen.

Structure Details

The NS5A protein is a zinc-binding and proline-rich hydrophilic phosphoprotein that is 56 kDa in weight and 448 amino acids long. The NS5A consists of four main regions: N-terminal amphipathic helix, Domain I, Domain II, and Domain III. In addition, low complexity sequences (LCIS1 and LCIS2) are interspersed between the three domains. Within hepatocytes infected with HCV, the NS5A protein localizes to the endoplasmic reticulum (ER) where it forms virus–induced multiple-membrane vesicles; in this region, known as the membranous web, the multiple-membrane vesicle hosts RNA replication complexes and lipid droplets.

Structure Details

The NS5B protein is 66 kDa in weight and 591 amino acids long. Similar to with other polymerases, NS5B has a conformation resembling a right hand with finger, palm, and thumb subdomains, with the enzyme conforming to a closed configuration during RNA synthesis and an open state during RNA elongation. The catalytic domain is formed by the N-terminal 530 amino acids. The HCV NS5B polymerase is structurally distinct from human cellular DNA and RNA polymerase enzymes. The NS5B protein contains the Gly-Asp-Asp motif in its active site and this region is binds magnesium, a process essential for enzymatic activity.