Fig. 4: Cryo-EM reconstruction of the T = 4 NCP formed with JQ707375.1 gRNA.

Centre: Atomic model of the front-half of the HBV T = 4 NCP shown as ribbon diagrams, coloured in yellow (A monomer), green (B monomer), blue (C monomer) and red (D monomer) for the quasi-equivalent monomers, and viewed along a two-fold axis built into the icosahedrally-averaged cryo-EM density map at 3.2 Å resolution (bar = 100 Å). Symbols indicate icosahedral symmetry axes. a–h Dashed (pink) circles indicate the locations of individual NCP symmetry axes, including the quasi-3-fold, and the arrows lead to boxes showing the transiting internal density associated with each of these locations. Cryo-EM density maps are shown as a grey mesh with the centre of the NCP towards the bottom. Cp atomic models are shown as sticks. Amino acid side-chains adjacent to the internal layer of density are indicated and coloured by heteroatom. The atomic model is fitted into the non-filtered shell of the Class 3 density map obtained after symmetry expansion and focused classification (a, c, e, g), and for clarity into the same map low-pass filtered to 5 Å (b, d, f, h), both shown at 1.5 σ. a, b Contacts located at three-fold vertices involve the E40-C48 sequence in Cp (including the E40-C43 alpha-helix and the S44-C48 loop) of three C monomers. The side chains of residues E40 and E46 are directly pointing to the internal density shell. c, d Contacts located at five-fold vertices involve five A monomers (pentamer). e, f Contacts located at quasi-three-fold vertices involve the E40-C48 sequence in Cp (including the E40-C43 alpha-helix and the S44-C48 loop) of one A monomer, one B monomer and one D monomer. The side chains of residues E40 and E46 point directly at the internal density shell. g, h Contacts located at two-fold vertices involve two C monomers and two D monomers (hexamer).