Cited by 710HIV Research and TreatmentSignaling Pathways in DiseaseHIV/AIDS drug development and treatment

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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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Background
Interactions of HIV-1 Capsid with Host Factors and Their Implications for Developing Novel Therapeutics
Zhuang, S., & Torbett, B. E. (2021) · Viruses · doi:10.3390/v13030417 · Cited by 53
“Cyclophilin A (CypA) is a peptidyl-prolyl cis-trans isomerase (PPIase), which binds to the flexible CypA-binding loop exposed on the top of CA N-terminal domain that protrudes from the capsid outer surface [43] (Figure 2).”
Background
The interdomain linker region of HIV-1 capsid protein is a critical determinant of proper core assembly and stability
Jiang, J., Ablan, S. D., Derebail, S. S., Hercík, K., Soheilian, F., Thomas, J. A., Tang, S., HEWLETT, I. K., Nagashima, K., Gorelick, R. J., et al. (2011) · Virology · doi:10.1016/j.virol.2011.09.012 · Cited by 57
“The N-terminal domain (NTD) of CA forms the hexameric lattice and each hexamer is linked to six others by interactions with C-terminal CA dimers (Briggs et al., 2006; Ganser et al., 1999; Ganser-Pornillos et al., 2004, 2007; Huseby et al., 2005; Lanman and Prevelige, 2005; Lanman et al., 2003; Li et al., 2000; Pornill…”
Influential
Simulated Self-Assembly of the HIV-1 Capsid: Protein Shape and Native Contacts Are Sufficient for Two-Dimensional Lattice Formation
Chen, B., & Tycko, R. (2011) · Biophysical Journal · doi:10.1016/j.bpj.2011.05.025 · Cited by 51
“The 146-residue NTD includes a b-hairpin and seven a-helices (37,38).”
Background
Structural and dynamical characterization of tubular HIV‐1 capsid protein assemblies by solid state nuclear magnetic resonance and electron microscopy
Chen, B., & Tycko, R. (2010) · Protein Science · doi:10.1002/pro.348 · Cited by 54
HIV Capsid Assembly, Mechanism, and Structure
Chen, B. (2016) · Biochemistry · doi:10.1021/acs.biochem.6b00159 · Cited by 57
Dynamic regulation of HIV-1 capsid interaction with the restriction factor TRIM5α identified by magic-angle spinning NMR and molecular dynamics simulations
Quinn, C. M., Wang, M., Fritz, M. P., Runge, B., Ahn, J., Xu, C., Perilla, J. R., Gronenborn, A. M., & Polenova, T. E. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1800796115 · Cited by 53
“As a result, the NTD harbors the interaction epitopes for restriction factors, such as cyclophilin A (CypA) and tripartite motif isoform 5α (TRIM5α) (13, 14).”
Background
Altered HIV-1 Gag Protein Interactions with Cyclophilin A (CypA) on the Acquisition of H219Q and H219P Substitutions in the CypA Binding Loop
Gatanaga, H., Das, D., Suzuki, Y., Yeh, D. D., Hussain, K. A., Ghosh, A. K., & Mitsuya, H. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m505920200 · Cited by 52
Investigation of N-Terminal Domain Charged Residues on the Assembly and Stability of HIV-1 CA
Douglas, C. C., Thomas, D. R., Lanman, J. K., & Prevelige, P. E. (2004) · Biochemistry · doi:10.1021/bi049359g · Cited by 51
“High-resolution structures of CA obtained by X-ray crystallography and NMR demonstrate that it is composed of structurally distinct N- and C-terminal domains ( 24-28 ).”
Human Immunodeficiency Virus Type 1 N-Terminal Capsid Mutants Containing Cores with Abnormally High Levels of Capsid Protein and Virtually No Reverse Transcriptase
Tang, S., Murakami, T., Cheng, N., Steven, A. C., Freed, E. O., & Levin, J. G. (2003) · Journal of Virology · doi:10.1128/jvi.77.23.12592-12602.2003 · Cited by 52
“Residues 85 to 93 in the exposed proline-rich loop (27, 73) constitute the binding site for CypA (49), a host peptidyl-prolyl cis-trans isomerase that is incorporated into virions (21, 54, 61).”
Background
Flexibility in HIV-1 Assembly Subunits: Solution Structure of the Monomeric C-Terminal Domain of the Capsid Protein
Alcaraz, L. A., del Álamo, M., Barrera, F. N., Mateu, M. G., & Neira, J. L. (2007) · Biophysical Journal · doi:10.1529/biophysj.106.101089 · Cited by 51
Crystal Structure of a Complex Between Human Spliceosomal Cyclophilin H and a U4/U6 snRNP-60K Peptide
Reidt, U., Wahl, M. C., Fasshauer, D., Horowitz, D. S., Lührmann, R., & Ficner, R. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00684-3 · Cited by 51
Structure of B-MLV Capsid Amino-terminal Domain Reveals Key Features of Viral Tropism, Gag Assembly and Core Formation
Mortuza, G. B., Dodding, M. P., Goldstone, D. C., Haire, L. F., Stoye, J. P., & Taylor, I. A. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.12.043 · Cited by 56
Virus–host interactomes — antiviral drug discovery
Ma‐Lauer, Y., Lei, J., Hilgenfeld, R., & von Brunn, A. (2012) · Current Opinion in Virology · doi:10.1016/j.coviro.2012.09.003 · Cited by 49
“(CA) is available [49] .”
Conformational Adaptation of Asian Macaque TRIMCyp Directs Lineage Specific Antiviral Activity
Ylinen, L. M. J., Price, A. J., Rasaiyaah, J., Hué, S., Rose, N. J., Marzetta, F., James, L. C., & Towers, G. J. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1001062 · Cited by 49
“). As stated above, there are two amino acid differences between the Cyp domain of Mafa TRIMCyp and the genomic CypA sequence, R69H and E143K. Superposition of the Mafa:HIV-1 complex with the previously solved wild-type CypA:HIV-1 structure (1AK4)”
Background
SUN2 Overexpression Deforms Nuclear Shape and Inhibits HIV
Donahue, D. A., Amraoui, S., Nunzio, F. D., Kieffer, C., Porrot, F., Opp, S., Diaz‐Griffero, F., Casartelli, N., & Schwartz, O. (2016) · Journal of Virology · doi:10.1128/jvi.03202-15 · Cited by 51
The ability of multimerized cyclophilin A to restrict retrovirus infection
Javanbakht, H., Diaz‐Griffero, F., Yuan, W., Yeung, D. F., Li, X., Song, B., & Sodroski, J. (2007) · Virology · doi:10.1016/j.virol.2007.04.034 · Cited by 50
“…with both the unprocessed HIV-1 Gag polyprotein and the processed capsid protein with low affinity (Franke et al., 1994; Thali et al., 1994; Gamble et al., 1996; Yoo et al., 1997), we show here that the ability of multimeric cyclophilin A to restrict retroviruses correlates with an…”
Background
Intracellular Trafficking of HIV-1 Cores: Journey to the Center of the Cell
Dvorin, J. D., & Malim, M. H. (2003) · Current topics in microbiology and immunology · doi:10.1007/978-3-642-19012-4_5 · Cited by 49
Virus Particle Core Defects Caused by Mutations in the Human Immunodeficiency Virus Capsid N-Terminal Domain
Scholz, I., Arvidson, B., Huseby, D. L., & Barklis, E. (2005) · Journal of Virology · doi:10.1128/jvi.79.3.1470-1479.2005 · Cited by 49
“Some of these defects may be attributable to altered interactions with cellular factors, such as cyclophilin A (CypA) (1, 2, 7, 9, 41), and host susceptibility factors, such as Ref1, Trim5 , and Lv1 (6, 12, 16, 17, 24, 32, 37).”
Background
HIV Capsid Protein Genetic Diversity Across HIV-1 Variants and Impact on New Capsid-Inhibitor Lenacapavir
Troyano-Hernáez, P., Reinosa, R., & Holguín, Á. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.854974 · Cited by 48
Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity
Kane, J. R., Stanley, D. J., Hultquist, J. F., Johnson, J. R., Mietrach, N., Binning, J. M., Jönsson, S., Barelier, S., Newton, B. W., Johnson, T. L., et al. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.04.038 · Cited by 49
“The motif bears some resemblance to the CYPA binding site of HIV-1 Capsid, 89GPIAP93 (Gamble et al., 1996), a GPxxP motif.”
In Vitro Assembly of Retroviruses
Bush, D. L., & Vogt, V. M. (2014) · Annual Review of Virology · doi:10.1146/annurev-virology-031413-085427 · Cited by 49
HIV-1 requires capsid remodelling at the nuclear pore for nuclear entry and integration
Guedán, A., Donaldson, C. D., Caroe, E. R., Cosnefroy, O., Taylor, I. A., & Bishop, K. N. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1009484 · Cited by 47
Active-site residues of cyclophilin A are crucial for its incorporation into human immunodeficiency virus type 1 virions
Dorfman, T., Weimann, A., Borsetti, A., Walsh, C. T., & Göttlinger, H. (1997) · Journal of Virology · doi:10.1128/jvi.71.9.7110-7113.1997 · Cited by 52
“Our results are consistent with the recently solved crystal structures of CyPA bound to the N-terminal domain of HIV-1 CA (15) and to a 25-mer fragment of HIV-1 CA (37).”
BackgroundResult
Host factors involved in resistance to retroviral infection
Takeuchi, H., & Matano, T. (2008) · Microbiology and Immunology · doi:10.1111/j.1348-0421.2008.00040.x · Cited by 48
Detailed characterization of a cyclophilin from the human malaria parasite Plasmodium falciparum
Berriman, M., & Fairlamb, A. H. (1998) · Biochemical Journal · doi:10.1042/bj3340437 · Cited by 48
An intracellular block to primate lentivirus replication
Stoye, J. P. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.192449399 · Cited by 48
The role of immunophilins in viral infection
Hopkins, S., & Gallay, P. A. (2014) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2014.11.011 · Cited by 47
Novel Inhibitor Binding Site Discovery on HIV-1 Capsid N-Terminal Domain by NMR and X-ray Crystallography
Goudreau, N., Lemke, C. T., Faucher, A., Grand‐Maître, C., Goulet, S., Lacoste, J., Rancourt, J., Malenfant, É., Mercier, J.-F., Titolo, S., et al. (2013) · ACS Chemical Biology · doi:10.1021/cb400075f · Cited by 46
Role of the Rous Sarcoma Virus p10 Domain in Shape Determination of Gag Virus-Like Particles Assembled In Vitro and within Escherichia coli
Joshi, S., & Vogt, V. (2000) · Journal of Virology · doi:10.1128/jvi.74.21.10260-10268.2000 · Cited by 49
“The first detailed model proposed to explain the tubular and spherical polymerization modes in vitro (35) invoked the presence or absence of the b-hairpin at the N terminus of mature CA (10, 15).”
Background
The dimerization domain of the HIV‐1 capsid protein binds a capsid protein‐derived peptide: A biophysical characterization
Garzón, M. T., Lidón‐Moya, M. C., Barrera, F. N., Prieto, A., Gómez, J., Mateu, M. G., & Neira, J. L. (2004) · Protein Science · doi:10.1110/ps.03555304 · Cited by 47
“Highresolution structures of both CA domains have been obtained (Gamble et al. 1996, 1997; Gitti et al. 1996).”
Background
A Mutation in Alpha Helix 3 of CA Renders Human Immunodeficiency Virus Type 1 Cyclosporin A Resistant and Dependent: Rescue by a Second-Site Substitution in a Distal Region of CA
Yang, R., & Aiken, C. (2007) · Journal of Virology · doi:10.1128/jvi.02634-06 · Cited by 44
“CypA is a cellular peptidylprolyl isomerase that binds to the HIV-1 CA NTD and is incorporated into virions through interaction with an exposed loop between helices 4 and 5 in HIV-1 and SIVcpz CA proteins (19, 27).”
Background
VSV-G pseudotyping rescues HIV-1 CA mutations that impair core assembly or stability
Brun, S., Solignat, M., Gay, B., Bernard, É., Chaloin, L., Fenard, D., Devaux, C. A., Chazal, N., & Briant, L. (2008) · Retrovirology · doi:10.1186/1742-4690-5-57 · Cited by 46
“According to structural studies, monomeric CA folds into two distinct globular domains: the N-terminal domain (NTD) (residues 1 to 145) and the C-terminal domain (CTD) (residues 151–231) are connected by a short flexible linker that folds in a 310 helix upon oligomerization of CA [16-19].”
Background
Complex Interplay between HIV-1 Capsid and MX2-Independent Alpha Interferon-Induced Antiviral Factors
Bulli, L., Apolonia, L., Kutzner, J., Pollpeter, D., Goujon, C., Herold, N., Schwarz, S.-M., Giernat, Y., Keppler, O. T., Malim, M. H., et al. (2016) · Journal of Virology · doi:10.1128/jvi.00458-16 · Cited by 46
“In addition to CypA (62, 63) and CPSF6 (56, 57), HIV-1 CA has been proposed to bind to the nuclear pore complex (NPC) protein NUP153 (64), as well as to the cyclophilin domain of NUP358 (51, 65), and binding-deficient CA mutants have been characterized.”
Background
Recognition of HIV-1 capsid by PQBP1 licenses an innate immune sensing of nascent HIV-1 DNA
Yoh, S. M., Mamede, J. I., Lau, D., Ahn, N., Sánchez-Aparicio, M. T., Temple, J. E., Tuckwell, A., Fuchs, N. V., Cianci, G. C., Riva, L., et al. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.06.010 · Cited by 47
Cells with High Cyclophilin A Content Support Replication of Human Immunodeficiency Virus Type 1 Gag Mutants with Decreased Ability To Incorporate Cyclophilin A
Ackerson, B. K., Rey, O., Canon, J. R., & Krogstad, P. A. (1998) · Journal of Virology · doi:10.1128/jvi.72.1.303-308.1998 · Cited by 45
“P217 is one of only nine CA residues which make a series of favorable contacts with the CyPA active site (17).”
Background
Proline Isomerization: From the Chemistry and Biology to Therapeutic Opportunities
Gurung, D., Danielson, J. A., Tasnim, A., Zhang, J., Zou, Y., & Liu, J. (2023) · Biology · doi:10.3390/biology12071008 · Cited by 50
“The N-terminal domain of the HIV-1 capsid (residues 1-151) has been captured complexed with CypA by X-ray crystallography [45] (PDB: 1AK4).”
BackgroundMethodInfluential
Gag Cytotoxic T Lymphocyte Escape Mutations Can Increase Sensitivity of HIV-1 to Human TRIM5α, Linking Intrinsic and Acquired Immunity
Battivelli, E., Migraine, J., Lecossier, D., Yéni, P., Clavel, F., & Hance, A. J. (2011) · Journal of Virology · doi:10.1128/jvi.05201-11 · Cited by 44
Novel cyclophilin D inhibitors derived from quinoxaline exhibit highly inhibitory activity against rat mitochondrial swelling and Ca2+ uptake/release
Guo, H., Feng, W. A. N. G., Yu, K., Chen, J., Bai, D., Chen, K., Shen, X., & Jiang, H. (2005) · Acta Pharmacologica Sinica · doi:10.1111/j.1745-7254.2005.00189.x · Cited by 45
Cyclophilin A enables specific HIV-1 Tat palmitoylation and accumulation in uninfected cells
Chopard, C., Tong, P. B. V., Tóth, P., Schatz, M., Yezid, H., Debaisieux, S., Mettling, C., Gross, A., Pugnière, M., Tu, A., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04674-y · Cited by 48
Structural Folds of Viral Proteins
Chapman, M. S., & Liljas, L. (2003) · Advances in protein chemistry · doi:10.1016/s0065-3233(03)01004-0 · Cited by 44
Recognition of protein substrates by the prolyl isomerase trigger factor is independent of proline residues 1 1Edited by P. E. Wright
Scholz, C., Mücke, M., Rapé, M., Pecht, A., Pahl, A. M., Bang, H., & Schmid, F. X. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1604 · Cited by 45

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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