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Asymmetric opening of HIV-1 Env bound to CD4 and a coreceptor-mimicking antibody

Nature Structural & Molecular Biology volume 26, pages 1167–1175 (2019)Cite this article

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A Publisher Correction to this article was published on 21 January 2020

A Publisher Correction to this article was published on 16 December 2019

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Abstract

The human immunodeficiency virus (HIV-1) envelope (Env) glycoprotein, a (gp120–gp41)3 trimer, mediates fusion of viral and host cell membranes after gp120 binding to host receptor CD4. Receptor binding triggers conformational changes allowing coreceptor (CCR5) recognition through CCR5’s tyrosine-sulfated amino (N) terminus, release of the gp41 fusion peptide and fusion. We present 3.3 Å and 3.5 Å cryo-EM structures of E51, a tyrosine-sulfated coreceptor-mimicking antibody, complexed with a CD4-bound open HIV-1 native-like Env trimer. Two classes of asymmetric Env interact with E51, revealing tyrosine-sulfated interactions with gp120 mimicking CCR5 interactions, and two conformations of gp120–gp41 protomers (A and B protomers in AAB and ABB trimers) that differ in their degree of CD4-induced trimer opening and induction of changes to the fusion peptide. By integrating the new structural information with previous closed and open envelope trimer structures, we modeled the order of conformational changes on the path to coreceptor binding site exposure and subsequent viral–host cell membrane fusion.

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Fig. 1: The Env protomers in E51–sCD4–BG505 complexes adopt two distinct conformations.
Fig. 2: E51 Fab interacts extensively with gp120.
Fig. 3: BG505 Env trimers are asymmetric in the class I and class II E51–sCD4–BG505 structures.
Fig. 4: Protomers A and B exhibit different structural features (see also Supplementary Video).
Fig. 5: gp41 exhibits different conformations in protomers A and B (see also Supplementary Video).
Fig. 6: Summary of conformational changes described in text between closed and various open Env conformations (see also Supplementary Video).

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Data availability

The structural coordinates were deposited into the Worldwide Protein Data Bank (wwPDB) with accession code 6U0L (class I E51–BG505 SOSIP.664–sCD4 complex) and 6U0N (class II E51–BG505 SOSIP.664–sCD4 complex). EM density maps were deposited into EMDB with accession numbers EMD-20605 (class I) and EMD-20608 (class II). Other data are available upon reasonable request.

Change history

  • 21 January 2020

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

  • 16 December 2019

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Acknowledgements

We thank M. Farzan, A.P. West and C.O. Barnes for helpful discussions. Structural studies were performed in the Biological and Cryogenic Transmission Electron Microscopy Center at Caltech with assistance from directors A. Malyutin and S. Chen. We thank the Gordon and Betty Moore and Beckman Foundations for gifts to Caltech to support electron microscopy, Z. Yu (Janeila Farm) for advice on cryo-EM, J. Vielmetter and the Caltech Protein Expression Center for protein production, and M. Shahgholi and the Caltech Protein Exploration Laboratory for mass spectrometry analyses. This work was supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health Grant No. HIVRAD P01 P01AI10014 (P.J.B.) and the National Institutes of Health Grant No. P50 8 P50 AI150464-13 (P.J.B.).

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Author notes

  1. Haoqing Wang

    Present address: Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA

  2. Albert Z. Liu

    Present address: Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA

Authors and Affiliations

  1. Division of Biology and Biological Engineering, California Institute of Technology, Pasadena CA, USA

    Zhi Yang, Haoqing Wang, Albert Z. Liu, Harry B. Gristick & Pamela J. Bjorkman

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Contributions

Z.Y. and P.J.B. conceived the study. Z.Y. solved and interpreted cryo-EM structures with help from H.W. Z.Y., H.W., H.B.G. and P.J.B. analyzed the data. A.Z.L. and H.B.G. prepared and isolated E51 Fabs. Z.Y. and P.J.B. wrote the paper with contributions from other authors.

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Correspondence to Pamela J. Bjorkman.

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Peer review information Beth Moorefield was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Extended data

Extended Data Fig. 1 Mass spectrometry characterization of E51 Fab.

a, Peak fractions from anion exchange chromatography of E51 Fab. b, Mass spectra of the three E51 peaks from panel a. The molecular mass for Peak 1 corresponded within 27 Da to the predicted mass for unmodified E51 Fab (48,791 Da), suggesting this E51 Fab fraction contained no sulfated tyrosines. The molecular masses for Peaks 2 and 3 were each increased by 80 Da from the preceding peak, corresponding to the molecular weight of a SO3− group (80 Da). These results are consistent with the identification of Peaks 2 and 3 as E51 Fab with one and two sulfated tyrosines, respectively. Peak 3 was used for preparing complexes for cryo-EM.

Extended Data Fig. 2 Data processing for BG505 SOSIP-sCD4-E51 complex structures.

a, Example of a motion-corrected and dose-weighted micrograph of E51-sCD4-BG505 complexes (representative individual particles in boxes). Scale bar = 50 nm. Defocus was ~2.6 μm underfocus. b, Data processing scheme. Collected micrographs were motion-corrected using MotionCor2 (ref. 1) without binning. Contrast transfer functions (CTFs) were estimated using Gctf 1.06 (ref. 2). ~1,000 particles were manually picked and subjected to 2D classification in RELION3,4. Particles from good classes were used as references for automatic particle picking using RELION AutoPicking. 941,841 autopicked particles were subjected to three rounds of reference-free 2D classification. In each round, particles from good 2D classes were selected, which gave 656,059 particles. Subsequently, using the Env trimer portion of an 80 Å low-pass filtered partially-open trimeric BG505 SOSIP structure (PDB 6CM3) as the reference model, first round of 3D classification was performed assuming C1 symmetry. Particles from good classes were combined and used for a second round of 3D classification with C1 symmetry. The resulting maps could be grouped into two classes: class I (320,895 particles) and class II (182,970 particles). Maps from the two classes were refined separately assuming C1 symmetry with the sCD4 D2 domain and E51 Fab CHCL domains masked out. After CTF refinement, movie refinement, and particle polishing, the class I and class II post-processed maps were refined to 3.3 Å and 3.5 Å resolution (FSC 0.143), respectively (Supplementary Fig. 3).

Extended Data Fig. 3 Validation of the BG505 SOSIP-sCD4-E51 complex structures.

Class I (panel a) and class II (panel b) E51-sCD4-BG505 complex structures. Top left in both panels: Gold-standard Fourier Shell Correlations (FSCs) of two classes of maps. Top right: Orientation distributions for class I and class II structures. Bottom: Local resolution estimations for class I and class II density maps (calculated using the local resolution program in RELION3,4).

Extended Data Fig. 4 Representative densities for class I and class II E51-sCD4-BG505 complex structures.

a, Densities for residues involved in E51 CDRH3 sulfotyrosine interactions. b, Densities for fusion peptides in protomers A (top) and B (bottom). c, Densities for HR1C helices in protomers A (top) and B (bottom).

Extended Data Fig. 5 Comparison of fusion peptide conformations in Env structures.

The fusion peptide is orange in the conformation A protomer, cyan in the conformation B protomer (from the E51-sCD4-BG505 complex structures reported here), teal in a partially-open 17b-sCD4-BG505-8ANC195 complex (PDB 6CM3), and pale cyan in a fully-open 17b-sCD4-B41 complex (PDB 5VN3). Fusion peptides from Env trimers in a closed, prefusion conformation are color coded as shown for their PDB IDs. References for structures are listed in Supplementary Table 2.

Supplementary information

Supplementary information

Supplementary Note 1 and Tables 1 and 2.

Reporting Summary

Supplementary Video

Asymmetric opening of HIV-1 Env trimer induced by CD4 revealed intermediate states. The first section of the video shows soluble HIV-1 Env trimer opening when bound to sCD4, as highlighted by conformational changes in gp120 V1V2 region, V3 and coreceptor binding region, as well as gp41 HR1C. The second section of the video shows CD4-induced protomer intermediate open states, which ultimately contribute to the asymmetric open states of Env trimer.

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Yang, Z., Wang, H., Liu, A.Z. et al. Asymmetric opening of HIV-1 Env bound to CD4 and a coreceptor-mimicking antibody. Nat Struct Mol Biol 26, 1167–1175 (2019). https://doi.org/10.1038/s41594-019-0344-5

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