Asymmetric conformations of cleaved HIV-1 envelope glycoprotein trimers in styrene-maleic acid lipid nanoparticles

doi:10.1038/s42003-023-04916-w

. 2023 May 18;6(1):535.

doi: 10.1038/s42003-023-04916-w.

Asymmetric conformations of cleaved HIV-1 envelope glycoprotein trimers in styrene-maleic acid lipid nanoparticles

Kunyu Wang^#^{1

2}, Shijian Zhang^#^{3

4}, Eden P Go⁵, Haitao Ding⁶, Wei Li Wang¹, Hanh T Nguyen^{3

4}, John C Kappes^{6

7}, Heather Desaire⁵, Joseph Sodroski^{8

9

10}, Youdong Mao^{11

12

13

14}

Affiliations

¹ State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, Beijing, China.
² Peking-Tsinghua Joint Center for Life Science, Peking University, Beijing, China.
³ Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
⁴ Department of Microbiology, Harvard Medical School, Boston, MA, USA.
⁵ Department of Chemistry, University of Kansas, Lawrence, KS, USA.
⁶ Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
⁷ Birmingham Veterans Affairs Medical Center, Research Service, Birmingham, AL, USA.
⁸ Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA. joseph_sodroski@dfci.harvard.edu.
⁹ Department of Microbiology, Harvard Medical School, Boston, MA, USA. joseph_sodroski@dfci.harvard.edu.
¹⁰ Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA. joseph_sodroski@dfci.harvard.edu.
¹¹ State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, Beijing, China. ymao@pku.edu.cn.
¹² Peking-Tsinghua Joint Center for Life Science, Peking University, Beijing, China. ymao@pku.edu.cn.
¹³ Center for Quantitative Biology, Academy of Advanced Interdisciplinary Studies, Peking University, Beijing, China. ymao@pku.edu.cn.
¹⁴ National Biomedical Imaging Center, Peking University, Beijing, China. ymao@pku.edu.cn.

^# Contributed equally.

PMID: 37202420
PMCID: PMC10195785
DOI: 10.1038/s42003-023-04916-w

Asymmetric conformations of cleaved HIV-1 envelope glycoprotein trimers in styrene-maleic acid lipid nanoparticles

Kunyu Wang et al. Commun Biol. 2023.

. 2023 May 18;6(1):535.

doi: 10.1038/s42003-023-04916-w.

Authors

Affiliations

¹ State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, Beijing, China.
² Peking-Tsinghua Joint Center for Life Science, Peking University, Beijing, China.
³ Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
⁴ Department of Microbiology, Harvard Medical School, Boston, MA, USA.
⁵ Department of Chemistry, University of Kansas, Lawrence, KS, USA.
⁶ Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
⁷ Birmingham Veterans Affairs Medical Center, Research Service, Birmingham, AL, USA.
⁸ Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA. joseph_sodroski@dfci.harvard.edu.
⁹ Department of Microbiology, Harvard Medical School, Boston, MA, USA. joseph_sodroski@dfci.harvard.edu.
¹⁰ Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA. joseph_sodroski@dfci.harvard.edu.
¹¹ State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, Beijing, China. ymao@pku.edu.cn.
¹² Peking-Tsinghua Joint Center for Life Science, Peking University, Beijing, China. ymao@pku.edu.cn.
¹³ Center for Quantitative Biology, Academy of Advanced Interdisciplinary Studies, Peking University, Beijing, China. ymao@pku.edu.cn.
¹⁴ National Biomedical Imaging Center, Peking University, Beijing, China. ymao@pku.edu.cn.

^# Contributed equally.

PMID: 37202420
PMCID: PMC10195785
DOI: 10.1038/s42003-023-04916-w

Abstract

During virus entry, the pretriggered human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer initially transits into a default intermediate state (DIS) that remains structurally uncharacterized. Here, we present cryo-EM structures at near-atomic resolution of two cleaved full-length HIV-1 Env trimers purified from cell membranes in styrene-maleic acid lipid nanoparticles without antibodies or receptors. The cleaved Env trimers exhibited tighter subunit packing than uncleaved trimers. Cleaved and uncleaved Env trimers assumed remarkably consistent yet distinct asymmetric conformations, with one smaller and two larger opening angles. Breaking conformational symmetry is allosterically coupled with dynamic helical transformations of the gp41 N-terminal heptad repeat (HR1_N) regions in two protomers and with trimer tilting in the membrane. The broken symmetry of the DIS potentially assists Env binding to two CD4 receptors-while resisting antibody binding-and promotes extension of the gp41 HR1 helical coiled-coil, which relocates the fusion peptide closer to the target cell membrane.

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Conflict of interest statement

The authors declare no competing interests.

Figures

**Fig. 1. Asymmetric structures of the AD8 and AE2 Env trimers.**
a Views of the AD8, AE2.1, and AE2.2 Env density maps along the trimer axis, from the perspective of the expressing cell/viral membrane. The individual protomers of the Env trimers are colored blue, green, and coral red. The schematic diagram on the left indicates the designations of the gp120 (a, c, and e) and gp41 (b, d, and f) chains and color scheme that will be used throughout the rest of the manuscript. The opening angles of each of the interprotomer interfaces in the AD8 and AE2.1 Env trimers are shown. The density associated with the gp41 membrane-proximal external regions (MPERs) and transmembrane (TM) regions in the AE2.2 map is colored yellow. b Side views of the AD8, AE2.1, and AE2.2 Env density maps, with the gp41 subunits at the top and the gp120 subunits at the bottom of the images. c, e The density maps of the AD8 (c) or AE2.1 (e) Envs fitted with asymmetric trimer models (left) or pseudo-C3 symmetric models (right) are shown. The structures of the Env protomers in the pseudo-C3 symmetric model are identical to those in the asymmetric model, except that the rotational angles between each pair of protomers was set to 120°. The pseudo-C3 symmetric models were fitted into the density of one protomer (Chains A and B). For all models, only the first mannose residue on each glycan is shown. d, f Map-model correlation coefficients (CC) for the symmetric and asymmetric models were calculated for each protomer of the AD8 (d) or AE2.1 (f) Env. The colors of the bars for the asymmetric models correspond to the colors of the chains in the maps and models. The overall residue CC (without glycans) was calculated for each protomer; the CC value shown is the average of the CC values of the three protomers.

**Fig. 2. Comparison of Env protomer conformations.**
a Molecular structures of the three protomers of the AD8 Env model were aligned using the gp120 subunits. The gp41 fusion peptide (FP), FPPR + HR1_N, HR1_C and α9 helix are colored violet, blue, red and orange, respectively. The inset shows that the α9 helices in the three protomers rotate through a range of 7.4°. b The molecular structures of the three protomers of the AE2.1 Env model, aligned and colored as in (a). The largest angle between two α9 helices is 11.7°. c The AD8 and AE2.1 Env trimer models were superimposed, based on alignment of one protomer (Chains C and D). In the superposed structures in the center, the AD8 Env model is colored gray and the AE2.1 model is colored according to the chain. The non-aligned protomers of the AE2.1 Env are closer to the trimer axis by 1.1 Å and 1.3 Å, relative to the corresponding AD8 Env protomers. Close-up side views of the density maps and models of an interprotomer interface with a larger opening angle (left) and a smaller opening angle (right) are shown, colored according to the chain. The HR1_N region is shown in the close-up views. HR1_N is an α-helix in the interprotomer interfaces with larger opening angles, whereas HR1_N in the interface with a smaller opening angle is either poorly ordered (for AD8) or a loop (for AE2.1). d The AD8 and Env(–) trimer models were superposed, based on alignment of one protomer (Chains C and D). In the left panel, the AD8 Env is in gray and Env(–) in purple. The interprotomer interface with a small opening angle is indicated with a star; one of the interprotomer interfaces with a large opening angle is indicated with a circle. Close-up side views of the interprotomer interfaces with a smaller opening angle (star) and a larger opening angle (circle) are shown in the right panels. In the right panels, the Env(–) model is colored purple; the AD8 Env model is colored gray, except for specific highlighted regions, colored as in (a).

**Fig. 3. Comparison of trimer geometry among different Env structures.**
a The interprotomer distances (in Å) between selected C_α atoms (Thr 336 and Gln 352) of gp120 (outer triangles) and Cα atoms (Trp 628 and Ile 635) of gp41 (inner triangles) are shown for the AD8 and AE2.1 Envs, Env(–) (PDB 7N6U) and an unliganded SOSIP Env trimer (PDB 4ZMJ). b The Cα–Cα distances shown in (a) are plotted for the gp120 and gp41 subunits. c The relationship between helicity of the FPPR–HR1_N region and the opening angle of the AD8, AE2.1 and Env(–) trimers is shown. The x axis represents the opening angle for each of the interprotomer interfaces, measured in PyMOL. The y axis represents the number of residues in an α-helical conformation for the FPPR–HR1_N region (residues Ser 534–Val 570) associated with an interprotomer interface. d The AE2.1 and Env(–) trimer models were superposed, based on alignment of AE2.1 gp120 (Chain E) with Env(–) gp120 (Chain B). The AE2.1 Env is colored gray and the Env(–) trimer is colored magenta. The opening angles of the Env(–) interprotomer interfaces are shown. e Comparison of the AE2.1 Env and the PGT151-bound HIV-1_JR-FL EnvΔCT structures (PDB 5FUU). The AE2.1 Env Chain E structure (in gray) is superposed on Chain C of the PGT151-bound HIV-1_JR-FL EnvΔCT structure (in salmon), with the PGT151 Fabs shown. The opening angles between the protomers of the PGT151-bound HIV-1_JR-FL EnvΔCT trimer are shown. f Comparison of the AE2.1 Env and the PGT151-bound HIV-1_AMC011 EnvΔCT structures (PDB 6OLP). The AE2.1 Env Chain E structure (in gray) is superposed on Chain C of the PGT151-bound HIV-1_AMC011 EnvΔCT structure (in green), with the PGT151 Fabs shown. The opening angles between the protomers of the PGT151-bound HIV-1_AMC011 EnvΔCT trimer are shown. d–f close-up side views of the interprotomer interfaces with a smaller opening angle (star) and a larger opening angle (circle) are shown in the insets. The close-up views show the gp41 fusion peptide, FPPR, HR1_N and HR1_C regions from the superposed protomers and the α9 helix from the adjacent protomer.

**Fig. 4. Comparison of CD4 binding to asymmetric and pseudo-symmetric Env trimers.**
a The gp120 chain of a gp120–CD4 complex (PDB 3JWO) was superposed on all three gp120 subunits of the asymmetric AE2.1 Env trimer (colored according to chains). The docked two-domain CD4 molecules are shown as magenta ribbons. Interprotomer interfaces 1 and 3 have larger opening angles; interprotomer interface 2 has a small opening angle. In interface 2, CD4 binding to the AE2.1 Env brings it into very close proximity to the glycans on Asn 301 modeled on the basis of the observed density map. b The panels in the left column show Asn 301 glycan structures from the AE2.1 model, with real cryo-EM density surrounding the yellow glycan residues. The panels in the right column show Asn 301 Man7 glycans with additional terminal mannose residues constructed in silico, colored the same as their associated Env protomers. At each interprotomer interface, any atoms on the Asn 301 glycans that are within 4 Å of CD4 are colored red. At interprotomer interface 3, the distance between the center of mass of the whole Man7 glycan and that of one β-sheet (Lys 2–Gly 6) on CD4 is 13.7 Å; the distance for the other β-sheet (Lys 166–Glu 169) on CD4 is 10.7 Å**. c** The gp120 chain of a gp120–CD4 complex (PDB 3JWO) was superposed on all three gp120 subunits of a C3 pseudo-symmetric AE2.1 Env trimer. This pseudo-symmetric AE2.1 Env structure is identical to the one used in Fig. 1e. CD4 is closer to the Asn 301 glycan on the adjacent protomer for the pseudo-symmetric AE2.1 trimer compared with its binding to the more open interfaces of the asymmetric AE2.1 trimer; however, no clash is encountered with the pseudo-symmetric trimer. d The left panel shows the Asn 301 glycan structure on one interprotomer interface of the C3 pseudo-symmetric AE2.1 Env trimer; the right panel shows the Asn 301 Man7 glycan with additional terminal mannose residues constructed in silico. Any atoms on the Asn 301 glycan that are within 4 Å of CD4 are colored red. The distance between the center of mass of the whole Man7 glycan and that of one β-sheet (Lys 2–Gly 6) on CD4 is 10.2 Å; the distance for the other β-sheet (Lys 166–Glu 169) on CD4 is 8.7 Å.

**Fig. 5. Env trimer tilting and Env ectodomain conformation.**
a The cryo-EM density map of the AE2.2 Env (green) shows the 16° tilt of the ectodomain with respect to the gp41 MPER and TM. Hierarchical 3D classification indicates conformational flexibility of this tilted state. The red dashed line represents the trimer axis; the black solid line represents the axis of a cylinder modeled into the MPER density. Two additional subclasses are shown, with the particle number used to generate each map and the estimated resolution. b The three interprotomer interfaces of the AE2.2 Env trimer are shown, with the chains colored according to the key. c A schematic diagram showing the spatial relationships of the FPPR–HR1_N (blue), HR1_C (red) and α9 helices (orange) on the AE2.1 Env trimer. The gp120 subunits are shown as a low-pass filtered surface. The two gp120 subunits flanking the interprotomer interface with the smallest opening angle are shaded brown. d A hypothetical model explaining how relaxation of the α9 helix regulates the formation of the DIS. The gp41 components are colored as in (c). When α9 is fixed by interaction with the MPER/membrane, its bonding to FPPR preserves the loop conformation of the associated HR1_N region (upper panel). When the interaction of α9 with the MPER is relaxed (e.g., by solubilization of Env, by Env tilting), α9 is free to interact with the nascent HR1_N helix (lower panel). The α9–HR1_N helix interactions stabilize the opening of the protomers to create the interfaces with opening angles of 123°–125°.

**Fig. 6. Antibody docking on a symmetric Env trimer and the more open interface of an asymmetric Env trimer.**
Models of antibody-bound complete Env trimers or subunits were aligned with the asymmetric AD8 trimer model or the symmetric HIV-1_BG505 SOSIP trimer model (PDB 4ZMJ), according to the gp120 chain. The gp120 of the Env–antibody complex was aligned to Chain E gp120 of the AD8 Env trimer that, along with Chain C gp120, flank an interprotomer interface with a larger opening angle (124°). AD8 models (Chain E is blue and Chain C is green) are on the left; HIV-1_BG505 SOSIP (wheat) models are on the right. The antibody heavy and light chains are colored with different shades of purple to allow them to be distinguished. The Env protomer bound by the antibody is shown with a molecular surface, and conflict residues in the adjacent Env protomer are shown in red. Conflict residues are defined as containing backbone atoms within 4 Å of any antibody atom. Details of the region of closest approach of antibody and the adjacent Env protomer are shown in the insets. The distances shown are measured between C_α atoms of selected residues in ChimeraX. The CD4BS antibodies include: a VRC01 (PDB 5FYK); b VRC03 (PDB 3SE8); c b13 (PDB 3IDY); d F105 (PDB 3HI1). VRC01 and VRC03 are CD4BS bNAbs, whereas b13 and F105 are CD4BS pNAbs.

**Fig. 7. A model involving an asymmetric HIV-1 Env trimer in virus entry.**
A model of the early steps in HIV-1 entry is shown, with the Env protomers colored as in Fig. 1 (MPER, gp41 membrane-proximal external region; α9, gp41 region spanning residues 628-664; FP, gp41 fusion peptide; FPPR, gp41 fusion peptide-proximal region; HR1_N and HR1_C, gp41 heptad repeat N- and C-terminal regions, respectively). The names of the functional Env trimer conformations are shown to the left of the figures, and the smFRET-defined conformations of the Env protomers are shown to the right of the figures^–. In the pretriggered Env conformation, the close association of the gp41 α9 region with the MPER hypothetically modulates the interaction between α9 and FPPR on the neighboring protomer. In turn, the interaction of FPPR and the adjacent HR1_N region with the gp120 inner domain contributes to the maintenance of the pretriggered conformation. Spontaneous transitions between the pretriggered conformation and the asymmetric default intermediate state (DIS) are governed by HIV-1 strain-dependent variables^,,,. Tilting of the DIS Env in the membrane is allosterically coupled to asymmetric displacement of the α9 helices, an increase in two of the opening angles between the protomers, and transitions of the associated HR1_N regions into helical conformations. In the asymmetric DIS, two protomers can bind CD4 with less steric hindrance and have more helical HR1_N regions. Thus, the DIS is predisposed to rearrange into the full CD4-bound conformation (the prehairpin intermediate), where the newly formed HR1_N helices extend the HR1_C coiled coil, relocating the fusion peptide (FP) closer to the target cell membrane. Binding the second receptor, CCR5, permits the prehairpin intermediate to form the six-helix gp41 bundle that mediates membrane fusion and virus entry. The six-helix bundle is composed of the HR1 coiled coil (HR1_N + HR1_C) and the HR2 helices, which include the α9 helix^–.

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References

1. Wyatt R, Sodroski J. The HIV-1 envelope glycoproteins: fusogens, antigens, and immunogens. Science. 1998;280:1884–1888. doi: 10.1126/science.280.5371.1884. - DOI - PubMed
1. Chen B. Molecular mechanism of HIV-1 entry. Trends Microbiol. 2019;27:878–891. doi: 10.1016/j.tim.2019.06.002. - DOI - PMC - PubMed
1. Willey RL, Bonifacino JS, Potts BJ, Martin MA, Klausner RD. Biosynthesis, cleavage, and degradation of the human immunodeficiency virus 1 envelope glycoprotein gp160. Proc. Natl Acad. Sci. USA. 1988;85:9580–9584. doi: 10.1073/pnas.85.24.9580. - DOI - PMC - PubMed
1. Zhang S, et al. Dual pathways of human immunodeficiency virus type 1 envelope glycoprotein trafficking modulate the selective exclusion of uncleaved oligomers from virions. J. Virol. 2021;95:e01369–20. doi: 10.1128/JVI.01369-20. - DOI - PMC - PubMed
1. Munro JB, et al. Conformational dynamics of single HIV-1 envelope trimers on the surface of native virions. Science. 2014;346:759–763. doi: 10.1126/science.1254426. - DOI - PMC - PubMed

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[1] Wyatt R, Sodroski J. The HIV-1 envelope glycoproteins: fusogens, antigens, and immunogens. Science. 1998;280:1884–1888. doi: 10.1126/science.280.5371.1884. - DOI - PubMed

[2] Wyatt R, Sodroski J. The HIV-1 envelope glycoproteins: fusogens, antigens, and immunogens. Science. 1998;280:1884–1888. doi: 10.1126/science.280.5371.1884. - DOI - PubMed

[3] Chen B. Molecular mechanism of HIV-1 entry. Trends Microbiol. 2019;27:878–891. doi: 10.1016/j.tim.2019.06.002. - DOI - PMC - PubMed

[4] Chen B. Molecular mechanism of HIV-1 entry. Trends Microbiol. 2019;27:878–891. doi: 10.1016/j.tim.2019.06.002. - DOI - PMC - PubMed

[5] Willey RL, Bonifacino JS, Potts BJ, Martin MA, Klausner RD. Biosynthesis, cleavage, and degradation of the human immunodeficiency virus 1 envelope glycoprotein gp160. Proc. Natl Acad. Sci. USA. 1988;85:9580–9584. doi: 10.1073/pnas.85.24.9580. - DOI - PMC - PubMed

[6] Willey RL, Bonifacino JS, Potts BJ, Martin MA, Klausner RD. Biosynthesis, cleavage, and degradation of the human immunodeficiency virus 1 envelope glycoprotein gp160. Proc. Natl Acad. Sci. USA. 1988;85:9580–9584. doi: 10.1073/pnas.85.24.9580. - DOI - PMC - PubMed

[7] Zhang S, et al. Dual pathways of human immunodeficiency virus type 1 envelope glycoprotein trafficking modulate the selective exclusion of uncleaved oligomers from virions. J. Virol. 2021;95:e01369–20. doi: 10.1128/JVI.01369-20. - DOI - PMC - PubMed

[8] Zhang S, et al. Dual pathways of human immunodeficiency virus type 1 envelope glycoprotein trafficking modulate the selective exclusion of uncleaved oligomers from virions. J. Virol. 2021;95:e01369–20. doi: 10.1128/JVI.01369-20. - DOI - PMC - PubMed

[9] Munro JB, et al. Conformational dynamics of single HIV-1 envelope trimers on the surface of native virions. Science. 2014;346:759–763. doi: 10.1126/science.1254426. - DOI - PMC - PubMed

[10] Munro JB, et al. Conformational dynamics of single HIV-1 envelope trimers on the surface of native virions. Science. 2014;346:759–763. doi: 10.1126/science.1254426. - DOI - PMC - PubMed

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Asymmetric conformations of cleaved HIV-1 envelope glycoprotein trimers in styrene-maleic acid lipid nanoparticles

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Asymmetric conformations of cleaved HIV-1 envelope glycoprotein trimers in styrene-maleic acid lipid nanoparticles

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