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Crystal Structure of Human Cyclophilin A Bound to the Amino-Terminal Domain of HIV-1 Capsid

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Gamble, Theresa R, Vajdos, Felix F, Yoo, Sanghee, Worthylake, David K, Houseweart, Megan, Sundquist, Wesley I, Hill, Christopher P·1996·Cell

DOI 10.1016/s0092-8674(00)81823-1

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Abstract

The HIV-1 capsid protein forms the conical core structure at the center of the mature virion. Capsid also binds the human peptidyl prolyl isomerase, cyclophilin A, thereby packaging the enzyme into the virion. Cyclophilin A subsequently performs an essential function in HIV-1 replication, possibly helping to disassemble the capsid core upon infection. We report the 2.36 A crystal structure of the N-terminal domain of HIV-1 capsid (residues 1-151) in complex with human cyclophilin A. A single exposed capsid loop (residues 85-93) binds in the enzyme's active site, and Pro-90 adopts an unprecedented trans conformation. The structure suggests how cyclophilin A can act as a sequence-specific binding protein and a nonspecific prolyl isomerase. In the crystal lattice, capsid molecules assemble into continuous planar strips. Side by side association of these strips may allow capsid to form the surface of the viral core. Cyclophilin A could then function by weakening the association between capsid strips, thereby promoting disassembly of the viral core.

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BackgroundInfluential
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Method
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Background
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“CypA interacts with HIV-1 CA at the G89-P90 peptide bond located on a nine amino acid flexible loop (P85-P93), and catalyses isomerisation of the bond [101,102].”
Background
Catalytic mechanism of cyclophilin as observed in molecular dynamics simulations: Pathway prediction and reconciliation of X‐ray crystallographic and NMR solution data
Trzesniak, D., & A, W. F. V. G. (2006) · Protein Science · doi:10.1110/ps.062356406 · Cited by 33
“When this project started, almost all model structures available had the ligand bound to cyclophilin in the cis conformation, except the model for the cyclophilin/HIV-1 capsid complex (Gamble et al. 1996; Vajdos et al. 1997; Zhao et al. 1997), which shows an N-terminal rotated trans ligand conformation.”
Background
How HIV-1 Gag Manipulates Its Host Cell Proteins: A Focus on Interactors of the Nucleocapsid Domain
Klingler, J., Anton, H., Réal, É., Zeiger, M., Moog, C., Mély, Y., & Boutant, E. (2020) · Viruses · doi:10.3390/v12080888 · Cited by 41
“CA-NTD is composed of 7 α-helices and a cyclophilin A (CypA)-binding loop with an N-terminus, which is unstructured in Gag but folded into aβ-hairpin in the mature CA [86,87].”
Background
Non‐Immunosuppressive Cyclophilin Inhibitors
Schiene‐Fischer, C., Fischer, G. S., & Braun, M. (2022) · Angewandte Chemie International Edition · doi:10.1002/anie.202201597 · Cited by 33
A Unique Spumavirus Gag N-terminal Domain with Functional Properties of Orthoretroviral Matrix and Capsid
Goldstone, D. C., Flower, T. G., Ball, N. J., Sanz-Ramos, M., Yap, M. W., Ogrodowicz, R. W., Stanke, N., Reh, J., Lindemann, D., Stoye, J. P., et al. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003376 · Cited by 32
Cyclophilin inhibitors as antiviral agents
Peel, M. R., & Scribner, A. W. (2013) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2013.05.101 · Cited by 32
The V86M mutation in HIV-1 capsid confers resistance to TRIM5α by abrogation of cyclophilin A-dependent restriction and enhancement of viral nuclear import
Veillette, M., Bichel, K., Pawlica, P., Freund, S. M. V., Plourde, M. B., Pham, Q. T., Reyes‐Moreno, C., James, L. C., & Berthoux, L. (2013) · Retrovirology · doi:10.1186/1742-4690-10-25 · Cited by 32
“Next, we determined the catalysed isomerisation rate of the G89-P90 bond in both WT and V86M capsids in the presence of CypA (Figure 6B).”
BackgroundInfluential
Modulation of HIV-1 infectivity and cyclophilin A-dependence by Gag sequence and target cell type
Matsuoka, S., Dam, E., Lecossier, D., Clavel, F., & Hance, A. J. (2009) · Retrovirology · doi:10.1186/1742-4690-6-21 · Cited by 32
“The mechanisms through which CypA binding modulates viral infectivity are not defined and several possibilities have been discussed, including effects on capsid stability, viral uncoating, and the protection of viral cores from cellular restriction factors [8,19-23].”
Background
An Integrative Bioinformatic Approach for Studying Escape Mutations in Human Immunodeficiency Virus Type 1gagin the Pumwani Sex Worker Cohort
Peters, H. O., Mendoza, M., Capina, R. E., Luo, M., Mao, X., Gubbins, M. J., Nagelkerke, N. J. D., MacArthur, I. C., Sheardown, B. B., Kimani, J., et al. (2007) · Journal of Virology · doi:10.1128/jvi.02742-06 · Cited by 32
“This study investigated the cyclophilin A binding loop in p24 (residues 217 to 225) (24) and identified a positively selected amino acid substitution at residue 223 from Ile to Val (n 89) in clade D-infected individuals.”
Background
Solution Properties of Murine Leukemia Virus Gag Protein: Differences from HIV-1 Gag
Datta, S. A. K., Zuo, X., Clark, P. K., Campbell, S. J., Wang, Y., & Rein, A. R. (2011) · Journal of Virology · doi:10.1128/jvi.05889-11 · Cited by 30
“MLV and HIV-1 Gag are similar to each other with respect to the secondary and tertiary structures of the MA, NTD, and CTD regions (18, 20, 22, 32, 35, 45); however, the linkers between these regions are apparently unstructured and/or flexible in HIV-1 Gag but rigid in MLV Gag.”
Background
Three Isoforms of Cyclophilin A Associated with Human Immunodeficiency Virus Type 1 Were Found by Proteomics by Using Two-Dimensional Gel Electrophoresis and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry
Misumi, S., Fuchigami, T., Takamune, N., Takahashi, I., Takama, M., & Shoji, S. (2002) · Journal of Virology · doi:10.1128/jvi.76.19.10000-10008.2002 · Cited by 32
“interaction sites that are located in the N-terminal domain of p24 around Gly89-Pro90 for packaging and in the C-terminal domain of p24 around Gly156-Pro157 and Gly223-Pro224 for destabilization of the capsid cone (5, 9).”
Background
Mutations within Four Distinct Gag Proteins Are Required To Restore Replication of Human Immunodeficiency Virus Type 1 after Deletion Mutagenesis within the Dimerization Initiation Site
Liang, C., Rong, L., Quan, Y., Laughrea, M., Kleiman, L., & Wainberg, M. A. (1999) · Journal of Virology · doi:10.1128/jvi.73.8.7014-7020.1999 · Cited by 32
“Crystal structure analysis of the CACypA complex shows that the side chain of Ile-91 projects directly out from the CypA active site and has no intermolecular contact (17).”
Background
Selected amino acid substitutions in the C-terminal region of human immunodeficiency virus type 1 capsid protein affect virus assembly and release
Abdurahman, S., Höglund, S., Goobar-Larsson, L., & Vahlne, A. G. (2004) · Journal of General Virology · doi:10.1099/vir.0.80137-0 · Cited by 32
“The N-terminal domain (aa 1–150) contributes to viral core formation and binds cyclophilin A, a cellular peptidyl–prolyl cis–trans isomerase (Gamble et al., 1996; Yoo et al., 1997).”
Background
Evaluation of HIV-1 capsid genetic variability and lenacapavir (GS-6207) drug resistance-associated mutations according to viral clades among drug-naive individuals
Nka, A. D., Bouba, Y., Této, G., Semengue, E. N. J., Takou, D., Ngueko, A. M. K., Fabeni, L., Carioti, L., Armenia, D., Pabo, W., et al. (2022) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkac388 · Cited by 31
Structure of a Monomeric Mutant of the HIV-1 Capsid Protein
Shin, R., Tzou, Y.-M., & Krishna, N. R. (2011) · Biochemistry · doi:10.1021/bi2011493 · Cited by 31
Ty3 Capsid Mutations Reveal Early and Late Functions of the Amino-Terminal Domain
Larsen, L. S. Z., Zhang, M., Beliakova‐Bethell, N., Bilanchone, V., Lamsa, A., Nagashima, K., Najdi, R., Kosaka, K., Kovacevic, V., Cheng, J. J., et al. (2007) · Journal of Virology · doi:10.1128/jvi.02207-06 · Cited by 31
“This is comparable to the structure-based helical compositions of HTLV-1, RSV, EIAV, and HIV-1, which are 57%, 58%, 60%, and 63%, respectively (8, 10, 17, 20, 34 , 35, 39, 48, 50, 51, 62, 63).”
MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions
Hayashi, T., Matsuzaki, Y., Yanagisawa, K., Ohue, M., & Akiyama, Y. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2073-x · Cited by 31
“PPIs are identified by biochemical experiments, such as the yeast two-hybrid method [4], mass spectrometry [5], and cocrystallization of protein complexes [6].”
Method
The Role of Capsid in HIV-1 Nuclear Entry
Guedán, A., Caroe, E. R., Barr, G. C. R., & Bishop, K. N. (2021) · Viruses · doi:10.3390/v13081425 · Cited by 29
“CypA canonically binds the CypA binding loop in the CA NTD (residues 85–93) [70].”
Background
Funnel Hunting in a Rough Terrain: Learning and Discriminating Native Energy Funnels
London, N., & Schueler‐Furman, O. (2008) · Structure · doi:10.1016/j.str.2007.11.013 · Cited by 31
HIV-1 capsid and viral DNA integration
Dwivedi, R., Prakash, P., Kumbhar, B. V., Balasubramaniam, M., & Dash, C. (2023) · mBio · doi:10.1128/mbio.00212-22 · Cited by 31
Dissecting the Microscopic Steps of the Cyclophilin A Enzymatic Cycle on the Biological HIV-1 Capsid Substrate by NMR
Bosco, D. A., Eisenmesser, E. Z., Clarkson, M. W., Wolf‐Watz, M., Labeikovsky, W., Millet, Ó., & Kern, D. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.08.001 · Cited by 30
Heterogeneous susceptibility of circulating SIV isolate capsids to HIV-interacting factors
Mamede, J. I., Sitbon, M., Battini, J., & Courgnaud, V. (2013) · Retrovirology · doi:10.1186/1742-4690-10-77 · Cited by 32
Mutant murine leukemia virus Gag proteins lacking proline at the N-terminus of the capsid domain block infectivity in virions containing wild-type Gag
Rulli, S. J., Muriaux, D. M., Nagashima, K., Mirro, J., Oshima, M., Baumann, J. G., & Rein, A. R. (2006) · Virology · doi:10.1016/j.virol.2005.12.012 · Cited by 31
The NH 2 -Terminal Domain of the Human T-Cell Leukemia Virus Type 1 Capsid Protein Is Involved in Particle Formation
Rayne, F., Bouamr, F., Lalanne, J. R., & Mamoun, R. Z. (2001) · Journal of Virology · doi:10.1128/jvi.75.11.5277-5287.2001 · Cited by 28
“Three-dimensional (3D) structural models of the N- and C-terminal parts and of the entire HIV-1 CA protein have been published (1, 10, 11, 16, 27).”
Background
Differential Dependence of the Infectivity of HIV-1 Group O Isolates on the Cellular Protein Cyclophilin A
Wiegers, K. J., & Kräusslich, H. (2002) · Virology · doi:10.1006/viro.2001.1347 · Cited by 30
Dynamic design: manipulation of millisecond timescale motions on the energy landscape of cyclophilin A
(2020) · doi:10.1039/c9sc04696h · Cited by 29
Non-Cleavage Site Gag Mutations in Amprenavir-Resistant Human Immunodeficiency Virus Type 1 (HIV-1) Predispose HIV-1 to Rapid Acquisition of Amprenavir Resistance but Delay Development of Resistance to Other Protease Inhibitors
Aoki, M., Venzon, D. J., Koh, Y., Aoki-Ogata, H., Miyakawa, T., Yoshimura, K., Maeda, K., & Mitsuya, H. (2009) · Journal of Virology · doi:10.1128/jvi.02539-08 · Cited by 29
“It is thought that CypA plays an essential role in the HIV-1 replication cycle (4, 35) by destabilizing the capsid (p24 Gag protein) shell during viral entry and uncoating (12) and/or by performing an additional chaperone function, thus facilitating correct capsid condensation during viral maturation (17, 39).”
Background
A novel inhibitor-binding site on the HIV-1 capsid N-terminal domain leads to improved crystallizationviacompound-mediated dimerization
Lemke, C. T., Titolo, S., Goudreau, N., Faucher, A., Mason, S. W., & Bonneau, P. R. (2013) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444913006409 · Cited by 30
“NMR and X-ray structures of the isolated domains, as well as dimeric, pentameric and hexameric assemblies, have been solved (Gamble et al., 1996; Gitti et al., 1996; Pornillos et al., 2009, 2011; Wong et al., 2008), thereby elucidating the detailed interactions that make up the capsid lattice…”
Background
Design of a Gag Pentapeptide Analogue that Binds Human Cyclophilin A More Efficiently than the Entire Capsid Protein: New Insights for the Development of Novel Anti-HIV-1 Drugs
Li, Q., Moutiez, M., Charbonnier, J., Vaudry, K., Ménèz, A., Quéméneur, É., & Dugave, C. (2000) · Journal of Medicinal Chemistry · doi:10.1021/jm9903139 · Cited by 29
Cyclophilin A Plays Distinct Roles in Human Immunodeficiency Virus Type 1 Entry and Postentry Events, as Revealed by Spinoculation
Saphire, A. C. S., Bobardt, M. D., & Gallay, P. A. (2002) · Journal of Virology · doi:10.1128/jvi.76.9.4671-4677.2002 · Cited by 29
“This notion arose from the observation that CypA is a cis-trans isomerase (11, 12) and that CypA binds CA (1, 10), the main component of the shell that surrounds the viral genome.”
Background
Repurposing of cyclophilin A inhibitors as broad-spectrum antiviral agents
Han, J., Lee, M. K., Jang, Y., Cho, W., & Kim, M. (2022) · Drug Discovery Today · doi:10.1016/j.drudis.2022.05.016 · Cited by 28
The Nucleocapsid Protein of the SARS Coronavirus: Structure, Function and Therapeutic Potential
Surjit, M., & Lal, S. K. (2009) · Springer eBooks · doi:10.1007/978-3-642-03683-5_9 · Cited by 28
“Notable is the fact that HIV-1 gag also binds with human cyclophylin A and this interaction is crucial for HIV infection (Gamble et al. 1996).”
Background
Investigation by Atomic Force Microscopy of the Structure of Ty3 Retrotransposon Particles
Kuznetsov, Y. G., Zhang, M., Menees, T. M., McPherson, A., & Sandmeyer, S. B. (2005) · Journal of Virology · doi:10.1128/jvi.79.13.8032-8045.2005 · Cited by 28
“in the context of an amino-terminal extension (22, 26, 59, 80).”
Background
Structural, Biochemical, and in Vivo Characterization of the First Virally Encoded Cyclophilin from the Mimivirus
Thai, V., Renesto, P., Fowler, C. A., Brown, D. J., Davis, T. L., Gu, W., Pollock, D. D., Kern, D., Raoult, D., & Eisenmesser, E. Z. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.08.051 · Cited by 28
trans-Complementation Rescue of Cyclophilin A-Deficient Viruses Reveals that the Requirement for Cyclophilin A in Human Immunodeficiency Virus Type 1 Replication Is Independent of Its Isomerase Activity
Saphire, A. C. S., Bobardt, M. D., & Gallay, P. A. (2002) · Journal of Virology · doi:10.1128/jvi.76.5.2255-2262.2002 · Cited by 28
“However, these sites are located in the C-terminal domain of CA, which is essential for CA oligomerization and CA core formation (7, 8, 15, 16, 19, 38).”
Background
The capsid protein of human immunodeficiency virus: designing inhibitors of capsid assembly
Neira, J. L. (2009) · FEBS Journal · doi:10.1111/j.1742-4658.2009.07314.x · Cited by 27
Gain-of-Sensitivity Mutations in a Trim5-Resistant Primary Isolate of Pathogenic SIV Identify Two Independent Conserved Determinants of Trim5α Specificity
McCarthy, K. R., Schmidt, A. G., Kirmaier, A., Wyand, A. L., Newman, R. M., & Johnson, W. E. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003352 · Cited by 27
“Of these, the structural basis for recognition of CA by rhTrim5 Cyp is best understood, and is attributed to interactions between the CypA domain and the 4–5 loop [65,66].”
Background
General Model for Retroviral Capsid Pattern Recognition by TRIM5 Proteins
Wagner, J. M., Christensen, D. E., Bhattacharya, A., Dawidziak, D. M., Roganowicz, M., Wan, Y., Pumroy, R. A., Demeler, B., Ivanov, D. N., Ganser‐Pornillos, B. K., et al. (2017) · Journal of Virology · doi:10.1128/jvi.01563-17 · Cited by 27
Self-citation
Diverse HIV viruses are targeted by a conformationally dynamic antiviral
Caines, M. E. C., Bichel, K., Price, A. J., McEwan, W. A., Towers, G. J., Willett, B. J., Freund, S. M. V., & James, L. C. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2253 · Cited by 27
Structural Determinants of the Anti-HIV Activity of a CCR5 Antagonist Derived from Toxoplasma gondii
Yarovinsky, F., Andersen, J. F., King, L. R., Caspar, P., Aliberti, J., Golding, H., & Sher, A. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m410550200 · Cited by 27
NMR Structure of the N-Terminal Domain of Capsid Protein from the Mason–Pfizer Monkey Virus
Macek, P., Chmelík, J., Křížová, I., Kadeřávek, P., Padrta, P., Žı́dek, L., Wildová, M., Hadravová, R., Chaloupková, R., Pichová, I., et al. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.06.029 · Cited by 27
Transient HIV-1 Gag–protease interactions revealed by paramagnetic NMR suggest origins of compensatory drug resistance mutations
Deshmukh, L., Louis, J. M., Ghirlando, R., & Clore, G. M. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1615342113 · Cited by 26
“, Lys30 and Arg76 of MA are involved in Gag–membrane interactions (30, 31), and His219 is located in an exposed loop within the N-terminal domain of CA loop that binds to cyclophilin-A (32)], implying multiple functions for these residues.”
Background
The Three-Fold Axis of the HIV-1 Capsid Lattice Is the Species-Specific Binding Interface for TRIM5α
Morger, D., Zosel, F., Bühlmann, M., Züger, S., Mittelviefhaus, M., Schuler, B., Luban, J., & Grütter, M. G. (2017) · Journal of Virology · doi:10.1128/jvi.01541-17 · Cited by 28
Cryoelectron Microscopic Examination of Human Immunodeficiency Virus Type 1 Virions with Mutations in the Cyclophilin A Binding Loop
Kong, L. B., An, D. S., Ackerson, B. K., Canon, J. R., Rey, O., Chen, I. S. Y., Krogstad, P. A., & Stewart, P. L. (1998) · Journal of Virology · doi:10.1128/jvi.72.5.4403-4407.1998 · Cited by 27
“Pro-231 is immediately adjacent to the residue Glu-230, which has been shown to be involved in the hinge motion of the exposed loop in crystal structures of CA interaction with CyPA (14).”
BackgroundResultInfluential
Mechanistic Independence of Nef and Cyclophilin A Enhancement of Human Immunodeficiency Virus Type 1 Infectivity
Aiken, C. (1998) · Virology · doi:10.1006/viro.1998.9254 · Cited by 27
“Nef contains a highly conserved PGPG sequence element that forms part of a turn on the protein surface (Lee et al., 1996; Shugars et al., 1993) that is reminiscent of the CyPA-binding domain of capsid (Gamble et al., 1996).”
Background

Authors: Gamble, T. R., Vajdos, F. F., Yoo, S., Worthylake, D. K., Houseweart, M., Sundquist, W. I., & Hill, C. P.
Affiliations: University of Utah (US)
Corresponding author: Hill, Christopher P
ORCID: Gamble, Theresa R
Vajdos, Felix F
Yoo, Sanghee
Sundquist, Wesley I
Hill, Christopher P
Venue: Cell
Publisher: Elsevier BV
Published: 1996-12
Volume: 87
Issue: 7
Pages: 1285-1294
ISSN: 0092-8674 (ISSN-L)
DOI: 10.1016/s0092-8674(00)81823-1
OpenAlex: W2121753315
Cited by: 706
References: 59
Citations by year: 2026: 12 · 2025: 8 · 2024: 7 · 2023: 18 · 2022: 20 · 2021: 26 · 2020: 16 · 2019: 12 · 2018: 23 · 2017: 21 · 2016: 29 · 2015: 22 · 2014: 25 · 2013: 32 · 2012: 24
FWCI: 6.27
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 6072 d)
Locations: Cell (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Signaling Pathways in Disease
Health Sciences › Medicine › Infectious Diseases › HIV/AIDS drug development and treatment
Keywords: cyclophilin A, HIV-1 capsid, peptidyl-prolyl isomerase, protein-protein complex, capsid disassembly, viral core, capsid assembly, HIV-1 replication
MeSH terms: Amino Acid Isomerases, Capsid, Carrier Proteins, Humans, Models, Molecular, Protein Binding, Virion, HIV-1, Gene Products, gag, Protein Structure, Tertiary, Crystallography, X-Ray, Peptidylprolyl Isomerase

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Crystal Structure of Human Cyclophilin A Bound to the Amino-Terminal Domain of HIV-1 Capsid

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