CoChat
Sign Up
Cited by 253HIV Research and TreatmentAdvanced Electron Microscopy Techniques and ApplicationsEnzyme Structure and Function

Structural Convergence between Cryo-EM and NMR Reveals Intersubunit Interactions Critical for HIV-1 Capsid Function

Open access
Byeon, In-Ja L., Meng, Xin, Jung, Jinwon, Zhao, Gongpu, Yang, Ruifeng, Ahn, Jinwoo, Shi, Jiong, Concel, Jason +3 more·2009·Cell
DOI 10.1016/j.cell.2009.10.010PMC PMC2782912
Open this paper in CoChat — free accountOpen PDF

Abstract

Mature HIV-1 particles contain conical-shaped capsids that enclose the viral RNA genome and perform essential functions in the virus life cycle. Previous structural analysis of two- and three-dimensional arrays of the capsid protein (CA) hexamer revealed three interfaces. Here, we present a cryoEM study of a tubular assembly of CA and a high-resolution NMR structure of the CA C-terminal domain (CTD) dimer. In the solution dimer structure, the monomers exhibit different relative orientations compared to previous X-ray structures. The solution structure fits well into the EM density map, suggesting that the dimer interface is retained in the assembled CA. We also identified a CTD-CTD interface at the local three-fold axis in the cryoEM map and confirmed its functional importance by mutagenesis. In the tubular assembly, CA intermolecular interfaces vary slightly, accommodating the asymmetry present in tubes. This provides the necessary plasticity to allow for controlled virus capsid dis/assembly.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.cell.2009.10.010

Cites

10 of 10 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Different retroviruses adopt distinct core geometries, and the cores within a single virus preparation can also vary in morphology.

    “Different retroviruses adopt distinct core geometries, and the cores within a single virus preparation can also vary in morphology”

    From Retrovirus maturation-an extraordinary structural transformation (2016) · cites this paper as [58]

    The Introduction (page unavailable) says HIV-1 capsids generally form cones while Rous sarcoma virus capsids form irregular polyhedra. The Results and Discussion (page unavailable) report varied morphologies in in-vitro HIV-1 capsid-protein assemblies, but do not establish that cores within a single virus preparation vary in morphology. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • The CA-CTDs are located beneath the hexameric ring and form dimeric inter-hexamer interactions involving mainly hydrophobic interactions between residues on helix 9 at the local twofold and residues on helix 10 at the local three-fold.

    “The CA-CTDs are located beneath the hexameric ring and form dimeric inter-hexamer interactions involving mainly hydrophobic interactions between residues on helix 9 at the local twofold [6,53] and residues on helix 10 at the local three-fold”

    From Retrovirus maturation-an extraordinary structural transformation (2016) · cites this paper as [54]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 41

  1. Aiken C 2009 Cell-free assays for HIV-1 uncoating Methods Mol Biol 485 41 53 19020817 PMC3842014
  2. Alcaraz LA del Alamo M Barrera FN Mateu MG Neira JL 2007 Flexibility in HIV-1 assembly subunits: solution structure of the monomeric C-terminal domain of the capsid protein Biophys J 93 1264 1276 17526561 PMC1929042
  3. Berthet-Colominas C Monaco S Novelli A Sibai G Mallet F Cusack S 1999 Head-to-tail dimers and interdomain flexibility revealed by the crystal structure of HIV-1 capsid protein (p24) complexed with a monoclonal antibody Fab Embo J 18 1124 1136 10064580 PMC1171204
  4. Bosco DA Kern D 2004 Catalysis and binding of cyclophilin A with different HIV-1 capsid constructs Biochemistry 43 6110 6119 15147195
  5. Briggs JA Simon MN Gross I Krausslich HG Fuller SD Vogt VM Johnson MC 2004 The stoichiometry of Gag protein in HIV-1 Nat Struct Mol Biol 11 672 675 15208690
  6. Briggs JA Wilk T Welker R Krausslich HG Fuller SD 2003 Structural organization of authentic, mature HIV-1 virions and cores Embo J 22 1707 1715 12660176 PMC152888
  7. Brunger AT 1992 Free R value: a novel statistical quantity for assessing the accuracy of crystal structures Nature 355 472 475 18481394
  8. Cardone G Purdy JG Cheng N Craven RC Steven AC 2009 Visualization of a missing link in retrovirus capsid assembly Nature 457 694 698 19194444 PMC2721793
  9. Clore GM Gronenborn AM 1998 Determining the structures of large proteins and protein complexes by NMR Trends Biotechnol 16 22 34 9470228
  10. Delaglio F Grzesiek S Vuister GW Zhu G Pfeifer J Bax A 1995 NMRPipe: a multidimensional spectral processing system based on UNIX pipes J Biomol NMR 6 277 293 8520220
  11. Egelman EH 2007 The iterative helical real space reconstruction method: surmounting the problems posed by real polymers J Struct Biol 157 83 94 16919474
  12. Erickson-Viitanen S Manfredi J Viitanen P Tribe DE Tritch R Hutchison CA 3rd Loeb DD Swanstrom R 1989 Cleavage of HIV-1 gag polyprotein synthesized in vitro: sequential cleavage by the viral protease AIDS Res Hum Retroviruses 5 577 591 2692658
  13. Forshey BM von Schwedler U Sundquist WI Aiken C 2002 Formation of a human immunodeficiency virus type 1 core of optimal stability is crucial for viral replication J Virol 76 5667 5677 11991995 PMC137032
  14. Gallay P Hope T Chin D Trono D 1997 HIV-1 infection of nondividing cells through the recognition of integrase by the importin/karyopherin pathway Proceedings of the National Academy of Sciences of the United States of America 94 9825 9830 9275210 PMC23276
  15. Ganser BK Li S Klishko VY Finch JT Sundquist WI 1999 Assembly and analysis of conical models for the HIV-1 core Science 283 80 83 9872746
  16. Hansen MR Mueller L Pardi A 1998 Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions Nat Struct Biol 5 1065 1074 9846877
  17. Herrmann T Güntert P Wüthrich K 2002 Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA J Mol Biol 319 209 227 12051947
  18. Ivanov D Tsodikov OV Kasanov J Ellenberger T Wagner G Collins T 2007 Domain-swapped dimerization of the HIV-1 capsid C-terminal domain Proc Natl Acad Sci U S A 104 4353 4358 17360528 PMC1838606
  19. Kelly BN Howard BR Wang H Robinson H Sundquist WI Hill CP 2006 Implications for viral capsid assembly from crystal structures of HIV-1 Gag(1-278) and CA(N)(133–278) Biochemistry 45 11257 11266 16981686
  20. Koradi R Billeter M Wuthrich K 1996 MOLMOL: a program for display and analysis of macromolecular structures J Mol Graph 14 51 55 29 32 8744573
  21. Lee W Revington MJ Arrowsmith C Kay LE 1994 A pulsed field gradient isotope-filtered 3D 13C HMQC-NOESY experiment for extracting intermolecular NOE contacts in molecular complexes FEBS Lett 350 87 90 8062930
  22. Li S Hill CP Sundquist WI Finch JT 2000 Image reconstructions of helical assemblies of the HIV-1 CA protein Nature 407 409 413 11014200
  23. Ludtke SJ Baldwin PR Chiu W 1999 EMAN: semiautomated software for high-resolution single-particle reconstructions J Struct Biol 128 82 97 10600563
  24. Momany C Kovari LC Prongay AJ Keller W Gitti RK Lee BM Gorbalenya AE Tong L McClure J Ehrlich LS 1996 Crystal structure of dimeric HIV-1 capsid protein Nature Structural Biology 3 763 770 8784350
  25. Nermut MV Hockley DJ Bron P Thomas D Zhang WH Jones IM 1998 Further evidence for hexagonal organization of HIV gag protein in prebudding assemblies and immature virus-like particles J Struct Biol 123 143 149 9843668
  26. Ottiger M Delaglio F Bax A 1998 Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra J Magn Reson 131 373 378 9571116
  27. Pettersen EF Goddard TD Huang CC Couch GS Greenblatt DM Meng EC Ferrin TE 2004 UCSF Chimera--a visualization system for exploratory research and analysis J Comput Chem 25 1605 1612 15264254
  28. Phillips JM Murray PS Murray D Vogt VM 2008 A molecular switch required for retrovirus assembly participates in the hexagonal immature lattice Embo J 27 1411 1420 18401344 PMC2374847
  29. Pornillos O Ganser-Pornillos BK Kelly BN Hua Y Whitby FG Stout CD Sundquist WI Hill CP Yeager M 2009 X-ray structures of the hexameric building block of the HIV capsid Cell 137 1282 1292 19523676 PMC2840706
  30. Rose S Hensley P O’Shannessy DJ Culp J Debouck C Chaiken I 1992 Characterization of HIV-1 p24 self-association using analytical affinity chromatography Proteins 13 112 119 1620693
  31. Sachse C Chen JZ Coureux PD Stroupe ME Fandrich M Grigorieff N 2007 High-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus J Mol Biol 371 812 835 17585939 PMC2025690
  32. Sattler M Maurer M Schleucher J Griesinger C 1995 A Simultaneous 15N, 1H-HSQC and 13C, 1H-HSQC with sensitivity enhancement and a heteronuclear gradient-echo J Biomol NMR 5 97 102 22911437
  33. Schwieters CD Kuszewski JJ Tjandra N Clore GM 2003 The Xplor-NIH NMR molecular structure determination package J Magn Reson 160 65 73 12565051
  34. Tang J Johnson JM Dryden KA Young MJ Zlotnick A Johnson JE 2006 The role of subunit hinges and molecular “switches” in the control of viral capsid polymorphism J Struct Biol 154 59 67 16495083
  35. Ternois F Sticht J Duquerroy S Krausslich HG Rey FA 2005 The HIV-1 capsid protein C-terminal domain in complex with a virus assembly inhibitor Nat Struct Mol Biol 12 678 682 16041386
  36. von Schwedler UK Stray KM Garrus JE Sundquist WI 2003 Functional surfaces of the human immunodeficiency virus type 1 capsid protein J Virol 77 5439 5450 12692245 PMC153941
  37. Wong HC Shin R Krishna NR 2008 Solution structure of a double mutant of the carboxy-terminal dimerization domain of the HIV-1 capsid protein Biochemistry 47 2289 2297 18220423
  38. Wright ER Schooler JB Ding HJ Kieffer C Fillmore C Sundquist WI Jensen GJ 2007 Electron cryotomography of immature HIV-1 virions reveals the structure of the CA and SP1 Gag shells Embo J 26 2218 2226 17396149 PMC1852790
  39. Yang R Aiken C 2007 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 J Virol 81 3749 3756 17267487 PMC1866112
  40. Yonekura K Toyoshima C 2000 Structure determination of tubular crystals of membrane proteins. II. Averaging of tubular crystals of different helical classes Ultramicroscopy 84 15 28 10896137
  41. Yonekura K Toyoshima C 2007 Structure determination of tubular crystals of membrane proteins. IV. Distortion correction and its combined application with real-space averaging and solvent flattening Ultramicroscopy 107 1141 1158 17368944

Cited by

Sorted by citations

Authors
Byeon, I.-J. L., Meng, X., Jung, J., Zhao, G., Yang, R., Ahn, J., Shi, J., Concel, J., Aiken, C., Zhang, P., & Gronenborn, A. M.
Affiliations
  • University of Pittsburgh (US)
  • Vanderbilt University (US)
Corresponding author
  • Zhang, Peijun
  • Gronenborn, Angela M.
ORCID
Venue
Cell
Publisher
Elsevier BV
Published
2009-11
Volume
139
Issue
4
Pages
780-790
ISSN
0092-8674 (ISSN-L)
DOI
10.1016/j.cell.2009.10.010
PMC
PMC2782912
OpenAlex
W2000218608
Cited by
253
References
10
Citations by year
2026: 8 · 2025: 9 · 2024: 9 · 2023: 8 · 2022: 4 · 2021: 15 · 2020: 13 · 2019: 17 · 2018: 12 · 2017: 21 · 2016: 22 · 2015: 19 · 2014: 15 · 2013: 21 · 2012: 18
FWCI
7.05
Type
journal article
Language
en
Open access
Licence
Locations
  • Cell (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • National Institutes of Health
  • National Institute of General Medical Sciences (P50GM082251, GM085043, R01GM085043, GM082251)
  • National Institute of Allergy and Infectious Diseases (AI076121, R56AI076121, R01AI076121)
Topics
  • Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
Keywords
HIV-1 capsid, intersubunit interactions, capsid disassembly, threefold symmetry, structural plasticity, cryo-EM density maps, NMR solution structure
MeSH terms
RNA, Viral, HIV-1, Virus Assembly, Nuclear Magnetic Resonance, Biomolecular, Cryoelectron Microscopy, Capsid Proteins

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review