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Crystal Structure of Human Cyclophilin A Bound to the Amino-Terminal Domain of HIV-1 Capsid
Open accessAbstract
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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“A beta-hairpin is formed by the N-terminal residues in mature-like CA, stabilized by a salt bridge between the N-terminal proline and a conserved aspartate in helix 3”
From Retrovirus maturation-an extraordinary structural transformation (2016) · cites this paper as [72]
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“There is a likely structural basis for the covariation in Gag, reflected by the fact that 10 of the 20 associations are between residues that are within 12 Å of each other (the maximum distance to permit hydrophobic interactions [33, 37]), both in the p24-CypA complex (12) and in the p24 hexameric protein structure (2…”
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BackgroundIdentification of HIV Inhibitors Guided by Free Energy Perturbation Calculations
Acevedo, O., Ambrose, Z., Flaherty, P. T., Aamer, H., Jain, P., & Sambasivarao, S. V. (2012) · Current Pharmaceutical Design · doi:10.2174/138161212799436421 · Cited by 23
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Konno, M., Sano, Y., Okudaira, K., Kawaguchi, Y., Yamagishi-Ohmori, Y., Fushinobu, S., & Matsuzawa, H. (2004) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.2004.04321.x · Cited by 21
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“CA proteins from N-tropic murine leukemia virus (N-MLV) (38), HIV-1 (18, 23), RSV (33), human T-cell leukemia virus type 1 (11, 32), and equine infectious anemia virus (31) all contain two domains, an elongated, tapered N-terminal domain (NTD) and a globular C-terminal domain (CTD) connected to each other by a flexibl…”
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“This disrupts CyPA-binding loop located at the N-terminal of HIV-1 CA protein [254] [255] [256] 263, 264 and inhibits HIV-1 infection in certain cell types.”
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“…methods for Rous sarcoma virus (RSV; Campos-Olivas et al., 2000), equine infectious anemia virus (EIAV; Jin et al., 1999), human T-cell leukemia virus (HTLV; Khorasanizadeh et al., 1999), and HIV-1 (Gamble et al., 1996, 1997; Gitti et al., 1996; Momany et al., 1996; Berthet-Colominas et al., 1999).”
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“Cyclophilin A (CypA) is a cellular peptidyl prolyl isomerase involved in protein folding and trafficking (23–25) and binds to HIV-1 CA (26, 27).”
Solbak, S. M. Ø., Reksten, T. R., Wray, V., Bruns, K., Horvli, O., Raae, A. J., Henklein, P., Henklein, P., Röder, R., Mitzner, D., et al. (2010) · BMC Structural Biology · doi:10.1186/1472-6807-10-31 · Cited by 18
“This binding motif is quite different from the sequence RHFPRIW found here that defines the binding region of N-terminal Vpr to CypA and also differs from the binding region of HIV-1 Capsid (HAGPIA), indicating that the Pro-dependent binding pocket of CypA is tolerant of substrates with several different sequences.”
BackgroundInfluentialCyclophilin function in Cancer; lessons from virus replication
Lavin, P. T., & Gee, M. M. M. (2015) · Current Molecular Pharmacology · doi:10.2174/1874467208666150519115443 · Cited by 18
“Incorporation is mediated through binding to the Gly-89-Pro-90 peptide bond of the N-terminal domain of newly assembled HIV-1 capsid (CA) [144]. p6 is a small protein that does not play a structural role in virion maturation, but it is required for virion incorporation of the viral accessory…”
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“The Gag protein contains several functionally and structurally distinct domains: the matrix (MA) domain at the N-terminal region of Gag, responsible for association with membrane (10, 25, 40, 57); the capsid (CA) domain at the central region, essential for GagGag interaction (7, 18, 20, 21, 56, 67); and the nucleocaps…”
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“while HIV CA crystallized as dimers (7, 20, 59).”
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“Cyclophilin A (CypA) is a peptidyl-prolyl isomerase that binds to the HIV-1 CA protein via a proline-rich loop, comprising CA residues 85 to 93, with glycine and proline at positions 89 and 90, respectively, serving as key binding motifs for CypA [50–52].”
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“…β-hairpin loop is stabilized by a salt bridge formed between a proline located at position 1 and an aspartic acid at position 51, on the NTD helix 3 (Gamble et al., 1996; Gitti et al., 1996, Gross et al., 1998; von Schwedler et al., 1998; Tang et al., 2002; Abdurahman et al., 2007; Monroe et al.,…”
BackgroundRole of Mason-Pfizer Monkey Virus CA-NC Spacer Peptide-Like Domain in Assembly of Immature Particles
Strohalmová, K., Spiwok, V., Lepšík, M., Hadravová, R., Křížová, I., Ulbrich, P., Pichová, I., Bednářová, L., Ruml, T., & Rumlová, M. (2014) · Journal of Virology · doi:10.1128/jvi.02286-14 · Cited by 16
Lokhandwala, P. M., Nguyen, T.-L. N., Bowzard, J. B., & Craven, R. C. (2008) · Virology · doi:10.1016/j.virol.2008.03.001 · Cited by 17
“1A, 1B) (Berthet-Colominas et al., 1999; Campos-Olivas et al., 2000; Cornilescu et al., 2001; Gamble et al., 1996; Gamble et al., 1997; Gitti et al., 1996; Jin et al., 1999; Khorasanizadeh et al., 1999; Kingston et al., 2000; Momany et al., 1996; Mortuza et al., 2004; Tang et al., 2002; Worthylake…”
BackgroundCellular restriction factors affecting the early stages of HIV replication
Perez, O., & Hope, T. J. (2006) · Current HIV/AIDS Reports · doi:10.1007/s11904-006-0004-3 · Cited by 17
Demange, L., Moutiez, M., Vaudry, K., & Dugave, C. (2001) · FEBS Letters · doi:10.1016/s0014-5793(01)02814-9 · Cited by 17
Human Cyclophilin Has a Significantly Higher Affinity for HIV-1 Recombinant p55 Than p24
Bristow, R., Byrne, J., Squirell, J., Trencher, H., Carter, T., Rodgers, B. C., Saman, E., & Duncan, J. (1999) · Journal of Acquired Immune Deficiency Syndromes & Human Retrovirology · doi:10.1097/00042560-199904010-00002 · Cited by 17
Emerging role of cyclophilin A in HIV-1 infection: from producer cell to the target cell nucleus
Padron, A., Prakash, P., Pandhare, J., Luban, J., Aiken, C., Balasubramaniam, M., & Dash, C. (2023) · Journal of Virology · doi:10.1128/jvi.00732-23 · Cited by 19
“Nevertheless, CypA has a higher affinity for multimeric CA relative to monomeric CA and thus has been suggested to preferentially bind assembled capsid (90, 95).”
BackgroundInfluentialCellular Restriction Factors of Feline Immunodeficiency Virus
Zielonka, J., & Münk, C. (2011) · Viruses · doi:10.3390/v3101986 · Cited by 16
“the viral core [75–78].”
Homology-based Identification of Capsid Determinants That Protect HIV1 from Human TRIM5α Restriction
Maillard, P. V., Zoete, V., Michielin, O. A., & Trono, D. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.187609 · Cited by 16
Wildová, M., Hadravová, R., Štokrová, J., Křížová, I., Ruml, T., Hunter, E., Pichová, I., & Rumlová, M. (2008) · Virology · doi:10.1016/j.virol.2008.07.021 · Cited by 16
“The capsid proteins are composed of two independently folded domains that are connected by short flexible linkers (Gamble et al., 1996; Momany et al., 1996; Gitti et al., 1996).”
BackgroundYu, X., Wang, Q., Yang, J.-C., Buch, I., Tsai, C., Ma, B., Cheng, S. Z. D., Nussinov, R., & Zheng, J. (2009) · Biomacromolecules · doi:10.1021/bm801151r · Cited by 16
Structure of recombinant human cyclophilin J, a novel member of the cyclophilin family
Huang, L.-L., Zhao, X.-M., Huang, C.-Q., Yu, L., & Xia, Z. (2005) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904033189 · Cited by 16
Lu, J., Bayro, M. J., & Tycko, R. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m116.720557 · Cited by 16
Taylor, W. R., Stoye, J. P., & Taylor, I. A. (2017) · BMC Structural Biology · doi:10.1186/s12900-017-0073-0 · Cited by 15
Fuchigami, T., Misumi, S., Takamune, N., Takahashi, I., Takama, M., & Shoji, S. (2002) · Biochemical and Biophysical Research Communications · doi:10.1016/s0006-291x(02)00329-7 · Cited by 16
Rits, M., van Dort, K. V., Münk, C., Meijer, A., & Kootstra, N. (2007) · Molecular Therapy · doi:10.1038/mt.sj.6300091 · Cited by 19
Hexagonal Organization of Moloney Murine Leukemia Virus Capsid Proteins
Mayo, K., McDermott, J., & Barklis, E. (2002) · Virology · doi:10.1006/viro.2002.1452 · Cited by 16
“…are consistent with those of CA NTD dimers from several different retroviruses (Berthet-Colominas et al., 1999; Campos-Olivas et al., 2000; Gamble et al., 1996; Gitti et al., 1996; Jin et al., 1999; Khorasanizadeh et al., 1999; Momany et al., 1996), supporting the notion that his-MoCA 2D…”
BackgroundCorrelation of Naturally Occurring HIV-1 Resistance to DEB025 with Capsid Amino Acid Polymorphisms
Gallay, P. A., Ptak, R. G., Bobardt, M. D., Dumont, J., Vuagniaux, G., & Rosenwirth, B. (2013) · Viruses · doi:10.3390/v5030981 · Cited by 15
“It binds specifically to a proline-containing loop formed by amino acids 85–93 of capsid protein p24 (CA) [10–12].”
BackgroundJuárez‐Jiménez, J., Tew, P., O’Connor, M. P., Llabrés, S., Sage, R., Glowacki, D. R., & Michel, J. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c00221 · Cited by 14
The Cysteine Residues of HIV-1 Capsid Regulate Oligomerization and Cyclophilin A-Induced Changes
Homme, M. B., Carter, C., & Scarlata, S. (2004) · Biophysical Journal · doi:10.1529/biophysj.104.053298 · Cited by 15
“Binding of CypA to CA, and catalysis of Pro-90 isomerization, has been previously characterized using a number of biophysical methods including fluorescence, NMR, crystallographic, and theoretical (Endrich et al., 1996; Gamble et al., 1996; Bosco et al., 2002; BonHomme et al., 2003; Agarwal, 2004; Bosco and Kern, 2004…”
BackgroundMethodInfluentialBennett, E. M., Lever, A. M. L., & Allen, J. F. (2004) · Journal of Virology · doi:10.1128/jvi.78.20.11303-11312.2004 · Cited by 15
“Cyclophilin A is incorporated into virions of HIV-1 through binding to a proline loop in the capsid domain (34), where it may promote viral core disassembly (18, 34) and may also modulate the response to cellular restriction factors (56).”
BackgroundChen, K., Piszczek, G., Carter, C., & Tjandra, N. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.425140 · Cited by 14
Taylor, G. M., Ma, L., Vogt, V. M., & Post, C. B. (2010) · Biochemistry · doi:10.1021/bi902196e · Cited by 14
Setiawan, L. C., van Dort, K. A., Rits, M. A. N., & Kootstra, N. A. (2015) · AIDS Research and Human Retroviruses · doi:10.1089/aid.2014.0361 · Cited by 14
Heyrana, K. J., Goh, B. C., Perilla, J. R., Nguyen, T.-L. N., England, M. R., Bewley, M. C., Schulten, K. J., & Craven, R. C. (2016) · Journal of Virology · doi:10.1128/jvi.00378-16 · Cited by 13
Self-Assembly of Fluorescent HIV Capsid Spheres for Detection of Capsid Binders
Lau, D., Walsh, J. C., Mousapasandi, A., Ariotti, N., Shah, V. B., Turville, S. G., Jacques, D. A., & Böcking, T. (2020) · Langmuir · doi:10.1021/acs.langmuir.0c00103 · Cited by 13
Goudreau, N., Coulombe, R., Faucher, A., Grand‐Maître, C., Lacoste, J., Lemke, C. T., Malenfant, É., Bousquet, Y., Fader, L. D., Simoneau, B., et al. (2013) · ChemMedChem · doi:10.1002/cmdc.201200580 · Cited by 14
Analysis of the retrovirus capsid interdomain linker region
Arvidson, B., Seeds, J. D., Webb, M., Finlay, L. A., & Barklis, E. (2003) · Virology · doi:10.1016/s0042-6822(02)00142-3 · Cited by 14
Abdurahman, S., Höglund, S., Höglund, A., & Vahlne, A. G. (2007) · Retrovirology · doi:10.1186/1742-4690-4-19 · Cited by 14
“Most of amino acid sequences in the CypA-binding loop of HIV-1 CA have been investigated using both genetic and structural studies [12,15-17].”
Fujita, M., Yoshida, A., Miyaura, M., Sakurai, A., Akari, H., Koyama, A. H., & Adachi, A. (2001) · Journal of Virology · doi:10.1128/jvi.75.21.10527-10531.2001 · Cited by 14
“The CyPA-binding loop of HIV-1 (14) is underlined.”
BackgroundEnzyme Selectivity Fine‐Tuned through Dynamic Control of a Loop
Vögeli, B., Bibow, S., & Celestine, N. (2016) · Angewandte Chemie International Edition · doi:10.1002/anie.201511476 · Cited by 15
Madlala, P., Singh, R., An, P., Werner, L., Mlisana, K. P., Karim, S. S. A., Winkler, C. A., & Ndung’u, T. (2016) · JAIDS Journal of Acquired Immune Deficiency Syndromes · doi:10.1097/qai.0000000000001028 · Cited by 14
“HIV-1 capsid (CA) directly interacts with the active sites of CypA through a prolyl peptide bond located in a proline-rich loop between the fourth and fifth helix loops and this leads to the incorporation of CypA into the HIV-1 virion capsid.(5,6) Disruption of the interaction between CypA and HIV-1, either by HIV-1 G…”
Hydrogen Bonding at a Conserved Threonine in Lentivirus Capsid Is Required for Virus Replication
Rue, S. M., Roos, J. W., Amzel, L. M., Clements, J. E., & Barber, S. A. (2003) · Journal of Virology · doi:10.1128/jvi.77.14.8009-8018.2003 · Cited by 14
“Using the coordinates of the HIV CA N-terminal domain (15), we constructed a homology model of SIV CA.”
BackgroundMethodInfluentialGuo, X., & Liang, C. (2005) · Virology · doi:10.1016/j.virol.2005.03.004 · Cited by 14
Sequence-based deep learning antibody design for in silico antibody affinity maturationPreprint
Kang, Y., Leng, D., Guo, J., & Pan, L. (2021) · arXiv (Cornell University) · doi:10.48550/arxiv.2103.03724 · Cited by 14
“The 3D structures of antibody complex 1BJ1 in Figure 1 - 4 are obtained from [19] and generated using molecular visualization system Pymol [21]”
HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation
Talledge, N., Yang, H., Shi, K., Coray, R., Yu, G., Arndt, W. G., Meng, S., Baxter, G. C., Mendonça, L., Castaño‐Díez, D., et al. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2023.168143 · Cited by 14
DockNet: high-throughput protein–protein interface contact prediction
Williams, N. P., Rodrigues, C. H. M., Truong, J. Q., Ascher, D. B., & Holien, J. K. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac797 · Cited by 12
Serrière, J., Robert, X., Perez, M., Gouet, P., & Guillon, C. (2013) · Retrovirology · doi:10.1186/1742-4690-10-64 · Cited by 13
“Hydrophobic Trp-Pro interactions have also been described in protein/protein interactions during HIV replication, for example in the interaction of HIV CA with cyclophilin A [53,54].”
BackgroundComparison of Biochemical Properties of HIV-1 and HIV-2 Capsid Proteins
Miyazaki, Y., Miyake, A., Doi, N., Koma, T., Uchiyama, T., Adachi, A., & Nomaguchi, M. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01082 · Cited by 14
“Moreover, the interaction of HIV CA with CypA or anti-retroviral TRIM-Cyp, known to promote HIV CA dissociation (Braaten et al., 1996a,b; Gamble et al., 1996; Forshey et al., 2005; Sebastian and Luban, 2005; Stremlau et al., 2006), was shown to be an exothermic event (Yoo et al.”
BackgroundInfluentialMAS NMR of HIV-1 protein assemblies
Suiter, C. L., Quinn, C. M., Lu, M., Hou, G., Zhang, H., & Polenova, T. E. (2015) · Journal of Magnetic Resonance · doi:10.1016/j.jmr.2014.12.009 · Cited by 14
The p12 Domain Is Unstructured in a Murine Leukemia Virus p12-CAN Gag Construct
Kyere, S. K., Joseph, P. R. B., & Summers, M. F. (2008) · PLoS ONE · doi:10.1371/journal.pone.0001902 · Cited by 13
Metadata
- 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
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 1996-12
- Volume
- 87
- Issue
- 7
- Pages
- 1285-1294
- ISSN
- 0092-8674 (ISSN-L)
- 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
- 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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