Structural biology of hepatitis C virus François Penin, PhD  Clinics in Liver Disease  Volume 7, Issue 1, Pages 1-21 (February 2003) DOI: 10.1016/S1089-3261(02)00066-1

Fig. 1 HCV genome organization, polyprotein processing, and protein structures. The genetic organization of hepatitis C virus (HCV) is schematically illustrated (top). The 5′ NTR consists of highly conserved 341 nucleotides (nt) sequence among HCV genotypes and possesses an internal ribosome entry site (IRES). It contains an RNA pseudoknot structure upstream of the initiation AUG codon, the latter being located in a loop of a stem-loop structure [103]. The 3′ NTR consists of a variable 40 nt sequence and an internal poly (U)/polypyrimidine tract followed by a 98 nt sequence well conserved among HCV genotypes and containing stable stem-loop structures [9]. 3′ NTR is thought to play an important role in the initiation of replication of viral genome. The central 9.6 kb open reading frame (ORF) code for a polyprotein of 3011–3033 aa depending on genotypes. The polyprotein processing and localization of HCV proteins relative to the ER membrane is schematically represented (middle). Transmembrane arrows indicate cleavages by the ER signal peptidase (black); cleavages by the NS3/NS4A proteinase complex (white); cleavage by signal peptide peptidase (gray); and autocatalytic cleavage of NS2–NS3 junction (cyclic). Arrows indicate the reorientation of C-terminal TMDs of E1 and E2 after signal peptidase cleavage. Asterisks denote glycosylations of the envelope proteins. The 10 protein products are shown with their approximate sizes and putative function. The number of amino acids for each protein of HCV genotypes 1 is given below in parenthesis: Core (191 aa); E1 (192 aa); E2 (363 aa); p7 (63 aa); NS2 (217 aa); NS3 (631 aa); NS3 Serine proteinase domain (189 aa); NS3 helicase domain (442 aa); NS4A (54 aa); NS4B (261 aa); NS5A (447 aa or so); and NS5B (591 aa). The alternative forms of core protein produced by ribosomal frameshift(s) are described in the text. Solved three-dimensional structures of HCV enzymes are shown (bottom). The PDB entry codes (http://www.rcsb.org/pdb/) of resolved RNA and protein structures are given below and on the figure in parenthesis: IRES RNA domains IIIc (1IDV) and IIId (1F84, 1F85, 1FQZ); core fragment 2–45 (1CWX); N-terminal segment of E1 transmembrane domain (1EMZ); NS3 serine proteinase domain free (1A1Q, 1BT7) or complexed with inhibitor (1DXW); NS3 serine proteinase domain complexed with NS4A fragment (1NS3, 1A1R, 1JXP, 1DXP) and inhibitors (1DY8, 1DY9); NS3 helicase domain-free (1HEI, 8OHM) and complexed with single-stranded DNA (1A1V); whole NS3 (1CU1); and NS5B ectodomain (1CSJ, 1QUV, 1C2P). Clinics in Liver Disease 2003 7, 1-21DOI: (10.1016/S1089-3261(02)00066-1)

Fig. 2 Hypothetical HCV life cycle. (1) Virus binding to cellular receptors. (2) Receptor-mediated endocytosis. (3) Low pH-dependant membrane fusion, nucleocapsid release. (4) Nucleocapsid uncoating. (5) IRES-mediated translation and polyprotein processing. (6) Membrane-associated RNA replication. (7) Virion formation and budding in intracellular vesicles. (8) Virion transport and maturation. (9) Virion release by exocytosis. ER, endoplasmic reticulum; (−), negative-stand RNA; (+), positive-strand RNA. Clinics in Liver Disease 2003 7, 1-21DOI: (10.1016/S1089-3261(02)00066-1)