A mature HIV particle cut in half, drawn to scale. Look at how few spikes there are and how far apart they sit. The spike itself is the real 5FYJ structure with a full sugar coat.
| Part | Status | Basis |
|---|---|---|
| Env spike, protein | atomic coordinates | PDB 5FYJ, three protomers, 14,967 heavy atoms1. Height and width are measured from the coordinates. |
| Env spike, glycans | modeled | One random draw of the Man9 shield from the full-density model (31 sites per protomer)2,3, 11,811 atoms. |
| Virion size, spike count | literature | Mean particle size about 145 nm (Briggs et al. 20034). Average of 14 ± 7 spikes per particle (Zhu et al.5), so the 4 and 35 buttons are not extremes of the model but the spread of the data. |
| Spike positions | random | Placed at random on the sphere with a minimum spacing. Each arrangement is one possible virion; the cut view and the outside view always show the same one. |
| Capsid | drawn | Cone about 60 nm across at the wide end, 20–30 nm at the narrow end; about 1,500 CA copies in roughly 250 hexamers and 12 pentamers6. Ticks on the wall mark the 9.6 nm hexamer spacing. Length and wall thickness are approximate. |
| Lipids, matrix, RNA, enzymes | drawn | Procedural shapes sized to be plausible, not atomic models. Bilayer thickness is about 4.6 nm in this drawing. |
| Antibody | atomic coordinates | PDB 1HZH, the intact human IgG1 b12 (Saphire et al. 20017), 151.6 kDa and about 15 nm across, drawn as one bead per residue plus the Fc sugars at the same scale as the spikes, both in the virion picture and in its own panel beside the spike close-up at the same scale. It is not docked to any spike, and its placement in the virion picture is a drawn choice. The amber sugars are the Fc glycans listed in 1HZH. b12 targets the CD4 binding site; it is not one of the six antibodies in this report. |
| Fabs on the spike | atomic coordinates | PDB 5FYJ as crystallized: PGT122 and 35O22 as full Fab chains, VRC01 as its variable domains only8,9,10. One copy per protomer, placed with the same symmetry operations as the spike. Sugars of the modeled shield that would overlap a shown Fab are hidden, which is an approximation. |
The cut removes the front half of the virion, along with any spikes that sat on it, so the picture shows only the spikes on the back half. Spike structure and glycan model come from the same work as the epitope atlas and the full-density shield in the main report.