Abstract
The mature retrovirus capsid consists of a variably curved lattice of capsid protein (CA) hexamers and pentamers. High-resolution structures of the curved assembly, or in complex with host factors, have not been available. By devising cryo-EM methodologies for exceedingly flexible and pleomorphic assemblies, we have determined cryo-EM structures of apo-CA hexamers and in complex with cyclophilin A (CypA) at near-atomic resolutions. The CA hexamers are intrinsically curved, flexible and asymmetric, revealing the capsomere and not the previously touted dimer or trimer interfaces as the key contributor to capsid curvature. CypA recognizes specific geometries of the curved lattice, simultaneously interacting with three CA protomers from adjacent hexamers via two noncanonical interfaces, thus stabilizing the capsid. By determining multiple structures from various helical symmetries, we further revealed the essential plasticity of the CA molecule, which allows formation of continuously curved conical capsids and the mechanism of capsid pattern sensing by CypA.
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Data availability
Cryo-EM density maps for CA A92E hexamers are deposited at the EMDB under accession codes EMD-10240 for (−13, 11), EMD-10228 for (−13, 12) and EMD-10239 for (−12, 11). Cryo-EM density maps for CypA-stabilized CA WT hexamers are deposited at the EMDB under accession codes EMD-10226 for (−13, 8), EMD-10246 for (−13, 12) and EMD-10229 for (−13,8) tube map. Cryo-EM density maps for the CypA/CA complexes are deposited at the EMDB under accession codes EMD-10740 (−13, 7), EMD-10739 (−13, 8), EMD-10742 (−13, 9), EMD-11176 (−13, 10), EMD-10738 (−8, 13) and EMD-10741 (−7, 13). Real-space refined atomic models of the CA hexamers are deposited at the Protein Data Bank under accession codes PDB 6SLU (−13, 11), PDB 6SKM (−13, 12), PDB 6SLQ (−12, 11), PDB 6SKK (−13, 8), PDB 6SMU (−13, 12) and PDB 6SKN (−13,8) tube. Real-space refined atomic models of the CypA/CA complexes are deposited at the Protein Data Bank under accession codes PDB 6Y9X (−13, 7), PDB 6Y9W (−13, 8), PDB 6Y9Z (−13, 9), PDB 6ZDJ (−13, 10), PDB 6Y9V (−8, 13) and PDB 6Y9Y (−7, 13). Source data are provided with this paper.
Code availability
The software is freely available from GitHub: https://github.com/kyledent/ArbitrEM.git.
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Acknowledgements
We thank C. Liu and J. Liu for help with initial manual data collection, Y. Cheng for access to the UCSF Polara and K2 detector, J. Dong and R. Esnouf for computer system support, J. Perilla for scientific discussion and T. Brosenitsch for critical reading of the manuscript. We thank D. Mastronarde for discussions regarding ArbitrEM development. This work was supported by the National Institutes of Health (P50AI150481, P.Z., C.A., A.N.E.), the UK Wellcome Trust Investigator Award 206422/Z/17/Z (P.Z.) and the UK Biotechnology and Biological Sciences Research Council grant BB/S003339/1 (P.Z.). S.G. is funded by a Wellcome Trust PhD Studentship. We acknowledge Diamond for access and support of the Cryo-EM facilities at the UK Electron Bio-Imaging Centre (eBIC, proposal EM14856 and NT21004, P.Z.), funded by the Wellcome Trust, MRC and BBSRC.
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Contributions
P.Z. conceived the research and, with A.N.E. and C.A., designed the experiments. K.D. developed ArbitrEM for automated targeted data collection. T.N. and J.N. prepared samples for cryo-EM. T.N., K.D. and G.Z. collected cryo-EM data. T.N., S.G. and G.Z. analyzed cryo-EM data. T.N. refined the atomic models. J.N. performed biochemical analysis and negatively stained EM. J.Z., J.S., J.A.-D. and W.L. performed virus infectivity assays and sectioning and imaging particle production. S.J. prepared primary CD4+ T cells and determined the intracellular concentration of CypA. T.N. and P.Z. analyzed atomic models and wrote the paper with support from all the authors.
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A.N.E. over the past 12 months has received fees from ViiV Healthcare, Co. for work unrelated to this topic. No other authors declare the potential for competing financial interests.
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Extended data
Extended Data Fig. 1 Automated targeted data collection flowchart.
a, The workflow of ArbitrEM, including two steps: target selection and automated data collection. (i) Low-magnification images are firstly acquired to identify holes where tubes are present, and these holes are selected by marking the holes in the images (red crosses); (ii) The images of selected holes are acquired at hole-magnification, centered, and converted into anchor maps; (iii) The acquisition points are marked on anchor maps (boxes), and the beam-image shifts to target the individual acquisition points are calculated. (iv) After all the targets are marked on the hole magnification images, the microscope uses the anchor maps and applies the total beam-image shifts (the stage shift combined with the target-specific beam-image shift) to acquire the high magnification movies. b, A typical low-magnification cryoEM image of CypA-stabilized WT CA assemblies. Scale bar, 2 μm. c, High-magnification image of CypA-stabilized WT CA tubular assembly, illustrating tubes are variable in diameter and easily deformed. d, Gallery of targeted images collected using ArbitrEM. Scale bars, 50 nm.
Extended Data Fig. 2 Data processing and 3D reconstruction flowchart for mature CA hexamer and CypA/CA complex.
a, Individual tubes are cropped from motion-corrected micrographs in EMAN2. b, Tubes are sorted based on their diameters. c, The FFT of each tube is calculated and used to determine helical symmetry. In these data, 12 different helical symmetries exist within a 3 nm diameter variation (red box in b). d, Segments from the same helical symmetry tubes are classified in RELION. e, Iterative Real Space Helical Reconstruction and RELION refinement for each helical symmetry are performed. f, Symmetry expansion and localized reconstruction of individual hexamers (dashed circle) from each tube segment are performed, and C2 symmetry is applied. g, After symmetry expansion, the CA density was subtracted, leaving only the local region of CA and CypA for further classification, as highlighted in the dashed magenta box in e). h, Localized reconstruction was performed to calculate the position of each sub-particle and the extracted sub-particles were subject to 3D-classification into 10 classes without alignment, with a regularization T factor of 10 and resolution limit of 8 Å. i, Classes showing clear features of CypA and CA density were selected, further classified into Mode 1 (one CypA, blue or orange) and Mode 2 (2 CypAs, blue-cyan or orange-pink). j, The Mode 2 classes were aligned and averaged (right), whereas CypA above dimer interface from both Mode 1 and Mode 2 were aligned and averaged (left) to yield the final density maps from each helical symmetry.
Extended Data Fig. 3 3D reconstructions of CA hexamer from five helical symmetries.
a, Electron density maps of CA tubes in the absence and presence of CypA and with different helical symmetries, as indicated. b, Fourier-shell-correlation (FSC) plots of CA hexamer density maps reconstructed from five helical symmetries. The highest resolution at FSC=0.143 is 3.6 Å from (-13, 8) symmetry. c, The FSC plot between the refined CA hexamer model and the 3.6 Å cryoEM density map from (-13, 8) symmetry. d, Representative density map from (-13, 8) symmetry overlapped with the refined atomic model, shown are the helices between adjacent CA monomers in different color. The map was contoured at 2𝜎.
Extended Data Fig. 4 Comparison of hexamers from CA A92E mutant and CypA-stabilized WT CA tubes with the same helical symmetry (-13, 12).
a, Overlay of rigid-body refined CA hexamers from CA A92E (cyan) and CypA-stabilized CA WT (gold) tubes. RMSD between two hexamers is 0.354 Å. CANTD and CACTD were rigid-body fitted into the density map independently. b, Overlay of a seven-hexamer lattice from a CA A92E tube with (-13, 12) symmetry (cyan) and that of a CypA-stabilized CA WT tube with the same symmetry (gold).
Extended Data Fig. 5 B-factors of the mature CA hexamer.
a–c, A sausage representation of B-factors mapped onto a CA monomer (a), hexamer (b), and tri-hexamer (c). The CypA-loop, H4-H5 loop, β-hairpin and H10 display high B-factors. d, e, Close-up views of a dimer interface (d) and a trimer interface (e) circled in (c). The width and coloring of the sausage are directly proportional to the B-factor, from blue (-30) to red (-100). CANTD, CA helices H1-3, CypA-loop, H4-H5 loop, β-hairpin and CACTD H10 are labeled.
Extended Data Fig. 6 Asymmetric and flexible configuration of CA in helical assemblies.
a, Distances between opposing CACTD domains in CA hexamer (measured between Cα of N195) from helical symmetry (-13, 8). b, Correlation plot of distances between CACTD domains versus hexamer array angles from five different helical assemblies. c, d, Close-up views of asymmetric β-hairpins (c, orange) and Arg18 residues adopting two conformations at the hexamer center (d). e, Overlay of electron density map with atomic model, showing two Arg18 side chain positions. f, Overlay of three Arg18 side chains in CA tubular structure (gold) with those in crystal structures in the absence of IP6 (blue, PDB 4WYM, PDB 4XFX, PDB 4XFY, PDB 4XFZ, PDB 5HGL). g, Overlay of Arg18 in crystal structures in complex with IP6 (PDB 6bht), same view as in f. 12 CA molecules from two hexamers (colored in pink and cyan, respectively) in one asymmetric unit were aligned on CANTD.
Extended Data Fig. 7 Binding of PF74 to CA hexamer and its effects on CA tubular assembly.
a, Light scattering of CA assemblies in the presence of PF74 at the indicated concentrations. b, Average number of tubes in each EM micrograph taken at the same magnification, with representatives shown in d–f. c, Distribution of the length of tubular assemblies in the presence of 0 µM (black), 10 µM (green) and 50 µM (pink) PF74. d–f, Representative images of negatively stained CA assemblies in the presence of 0 µM (d), 10 µM (e) and 50 µM (f) PF74. Scale bars, 0.5 µm. g, Atomic model of CA hexamer, clipped to show CANTD. Each CA monomer is labeled. The vertical dashed line indicates the tube axis. h–j, Overlay of density map with atomic model, showing the position of Arg173, which is critical for the binding of PF74 to hexamer57. Three CANTD-CACTD interfaces within the CA hexamer are shown between chains A-F (h), chains B-A (i) and chains C-B (j). Intermolecular hydrogen bonds between CACTD and CANTD are marked by red dashed lines with corresponding distances indicated. k, Overlay of WT and PF74-bound CA crystal structures, colored in grey and cyan, respectively. l, Overlay of three different PF74 pockets from the asymmetric hexamer in (-13,8) helical symmetry with crystal structures (PDB 4XFX and PDB 4XFZ). Arg173 side chains are shown in gold, red and blue, corresponding to panels h–j. The chain C-B interface is more similar to the crystal structure than are the chain A-F and chain B-A interfaces.
Extended Data Fig. 8 Analysis of CA mutant on virion morphologies and CA assemblies by TEM.
a, Representative images of mature, immature, empty, and eccentric particle morphologies; particles with 1-3 eccentric nucleoids alongside an otherwise electron-lucent core structure were grouped together. Magnification is 30,000X (scale bar, 100 nm). b, Quantitation of core morphology frequencies (average ± SD for n = 2 experiments) for WT and indicated mutant viruses. More than 200 particles were counted for each. Two-tailed Student’s t-test revealed significant differences for indicated categories versus the WT (****, P < 0.0001; ***, P < 0.001; **, P < 0.01; *, P < 0.05). For V181T, only 14 particles (predominantly immature) were observed in total. V181T was accordingly omitted from the graph and statistical analyses. c–g, Negative-stained images of WT and mutant CA assemblies. V181C forms two-dimensional crystalline sheets, whereas V181D forms tubular assemblies with much smaller diameters compared to WT tubes (17 nm vs 50 nm). Other mutants failed to form ordered assemblies. h, i, Close-up view of WT (h) and V181D (i) assemblies on the same scale. Scale bars, 200 nm in c–g, 50 nm in h, i.
Extended Data Fig. 9 3D reconstruction of CypA/CA complexes. Local resolution estimation of CypA/CA complex from different helical symmetries.
a, Local resolution estimation of CypA/CA complex from four different helical symmetries, colored by local resolution from blue to red. b, Fourier-shell-correlation (FSC) plots of CypA/CA density maps reconstructed from four helical symmetries. The highest resolution at FSC=0.143 is 4.0Å from (-13, 8) symmetry. c, Gallery of CypA/CA complexes. Eight helical reconstructions are shown in cross-sectional view (left) and face-on view (middle). Density maps are colored by the radius, with regions corresponding to CACTD, CANTD and CypA colored in yellow, green and blue, respectively. The outer diameters of the tubes are indicated. Enlarged views from regions marked by red dashed ovals are shown on the right.
Extended Data Fig. 10 Semi-quantitative analysis of CypA levels in primary CD4+ T cells.
a, CD4+ T cell CypA levels from two different blood donors (labeled D1 and D2) were compared by immunoblotting versus a dilution series of purified recombinant CypA protein. Where indicated, cells were cultured with 5 μg/ml of phytohaemagglutinin (+PHA) for 48 h prior to lysis. Lamin B1 was monitored as a loading control. Approximate ng amount of Cyclophilin A in each of the last four lanes is marked in red color. b, Signal intensity of each band in the dilution series in A was plotted against protein amount to generate a standard curve. Uncropped blot images are available as source data.
Supplementary information
Supplementary Information
Supplementary Table 1.
Supplementary Video 1
Overview of CypA/CA complex on top of dimer and trimer interfaces.
Supplementary Video 2
Overview of CypA-decorated tubular assembly of HIV capsid.
Supplementary Video 3
Overview of CypA-decorated conical HIV capsid.
Source data
Source Data Fig. 2
Uncropped SDS–PAGE.
Source Data Extended Data Fig. 10
Uncropped immunoblot images.
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Ni, T., Gerard, S., Zhao, G. et al. Intrinsic curvature of the HIV-1 CA hexamer underlies capsid topology and interaction with cyclophilin A. Nat Struct Mol Biol 27, 855–862 (2020). https://doi.org/10.1038/s41594-020-0467-8
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DOI: https://doi.org/10.1038/s41594-020-0467-8
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