Hepatitis C Virus Structure: Defined by What It Is Not

Abstract

Hepatitis C virus (HCV) represents an important and growing public health problem, chronically infecting an estimated 70 million people worldwide. This blood-borne pathogen is generating a new wave of infections in the United States, associated with increasing intravenous drug use over the last decade. In most cases, HCV establishes a chronic infection, sometimes causing cirrhosis, end-stage liver disease, and hepatocellular carcinoma. Although a curative therapy exists, it is extremely expensive and provides no barrier to reinfection; therefore, a vaccine is urgently needed. The virion is asymmetric and heterogeneous with the buoyancy and protein content similar to low-density lipoparticles. Core protein is unstructured, and of the two envelope glycoproteins, E1 and E2, the function of E1 remains enigmatic. E2 is responsible for specifically binding host receptors CD81 and scavenger receptor class B type I (SR-BI). This review will focus on structural progress on HCV virion, core protein, envelope glycoproteins, and specific host receptors.

Figure 1.

Schematic representations of various models of the hepatitis C virus (HCV) virion. (A) Complete icosahedral shell of E1/E2 heterodimers (purple and orange, respectively), embedded in a lipid bilayer (gray), and including an asymmetrically localized condensate of lipid-embedded core protein (green/yellow) and genomic RNA (magenta). (B–D) Colors and nucleocapsid representation as in panel A. (B) Incomplete or nonicosahedral organization of the E1/E2 heterodimers, embedded in a lipid bilayer. (C) Partial dissociation of the lipid bilayer by cholesterol ester (white/blue) with clustering of E1/E2 heterodimers in the remaining lipid bilayer. (D) Inclusion of host apolipoproteins ApoAI (dark gray), ApoB-100 (light blue), and ApoE (green).

Figure 2.

Structure and membrane association of core, E1, and E1 proteins. (A) A schematic of core (green/yellow), E1 (purple), and E2 (orange) proteins in association with the endoplasmic reticulum (ER) membrane (gray). Residues are numbered at feature boundaries and signal peptide peptidase (SPP) cleavage is indicated (scissors). Unusual residue content is noted for the core amino-terminal domain and core carboxy-terminal domain and signal sequences (SSs), and transmembrane helices (TMs) are located in the ER membrane. Ribbon diagrams of three of six partial E1 ectodomain subunits are colored by chain (pink, purple, and dark purple, respectively) to indicate the two potential dimerization interfaces (PDB ID 4UOI). Superimposed ribbon diagrams of three successively larger E2 ectodomains show mutual consistency (orange, yellow, and white are PDB IDs 4WEB, 4MWF, and 6MEI, respectively). Ribbon diagrams of an E1 (B) and an E2 (C) ectodomain, rainbow colored from amino (blue) to carboxyl (red) termini with highly variable regions in white and boundary residues as marked.

Figure 3.

Structure of CD81 with emphasis on the large extracellular loop (LEL). (A) The CD81 LEL forms a dimer in solution as well as in several crystals forms. A ribbon representation of the CD81 LEL dimer (PDB ID 1G8Q) with the individual molecules colored gray and in a rainbow from the amino terminus (blue) to the carboxyl terminus (red). The two disulfides are shown as sticks. Helices C and D as well as the intervening loop have been implicated in recognizing HCV E2. The LEL forms a head-to-tail dimer with the E2-binding sites on opposite ends of the complex. (B) The LEL dimeric interface with one molecule shown in a ribbon representation similar to panel A, whereas the second molecule is a surface rendition colored for electrostatic potential (red for negative, blue for positive, and white for neutral). (C) Ribbon rendition of the full-length, human CD81 structure (PDB ID 5TCX) modeled approximately on to an idealized lipid bilayer (stick representation) (a simulated dipalmitoylphosphatidylcholine bilayer). The transmembrane (TM) helices are colored beige, whereas the LEL is colored as a rainbow. The small extracellular loop (SEL) is located between TM helices 1 and 2, while the LEL is located between TMs 3 and 4. The five helices in the LEL are labeled A–E. The SEL is present in the crystallization construct, but disordered. Cholesterol from the crystallization solution is rendered as a space-filled model (left). A single molecule of bound cholesterol is shown in a sphere representation between the four TMs. (D) Superposition of the full-length CD81 structure (beige) with the LEL dimer colored blue and green for the two molecules in the asymmetric unit. (E) The LEL of the full-length CD81 has been proposed to undergo an open-to-closed transition upon cholesterol (green ligand) binding, the reverse of a closed-to-open transition modeled using molecular dynamics (Zimmerman et al. 2016). The coloring used is similar to panel A.

Figure 4.

Structure of scavenger receptor class B type I (SR-BI) homologs, CD36, and lysosomal integral membrane protein-2 (LIMP-2). (A) Ribbon representation of LIMP-2 with a gray surface highlighting a solvent-exposed cavity that traverses the protein from extracellular to the cell membrane. (B) Superposition of CD36 bound to PfEMP1 (PDB ID 5LGD) and LIMP-2 complexed with EV71 (PDB ID 6I2K). LIMP-2 is rainbow colored from the amino (blue) to the carboxyl (red) termini similar to panel A, whereas pfEMP1, EV71, and CD36 are colored red, pink, and gray, respectively. The structures are modeled on to an idealized lipid bilayer with the TMs. The lipid bilayer and amino-linked glycans are shown in a stick representation, whereas the TMs are approximated by blue (amino-terminal) and red (carboxy-terminal) cylinders.