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- EMDB-29777: Defective HIV-1 CA pentamer in surrounding hexameric lattice -

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Basic information

Entry
Database: EMDB / ID: EMD-29777
TitleDefective HIV-1 CA pentamer in surrounding hexameric lattice
Map data
Sample
  • Complex: Defective HIV-1 capsid (CA) pentamer within surrounding hexameric CA lattice
    • Other: Capsid protein
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsHighland CM / Dick RA
Funding support United States, United Kingdom, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI147890 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5U54AI150472-09 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54AI170855-01 United States
National Science Foundation (NSF, United States)DMR-1719875 United States
Medical Research Council (MRC, United Kingdom)MC_UP_1201/16 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structural insights into HIV-1 polyanion-dependent capsid lattice formation revealed by single particle cryo-EM.
Authors: Carolyn M Highland / Aaron Tan / Clifton L Ricaña / John A G Briggs / Robert A Dick /
Abstract: The HIV-1 capsid houses the viral genome and interacts extensively with host cell proteins throughout the viral life cycle. It is composed of capsid protein (CA), which assembles into a conical ...The HIV-1 capsid houses the viral genome and interacts extensively with host cell proteins throughout the viral life cycle. It is composed of capsid protein (CA), which assembles into a conical fullerene lattice composed of roughly 200 CA hexamers and 12 CA pentamers. Previous structural analyses of individual CA hexamers and pentamers have provided valuable insight into capsid structure and function, but detailed structural information about these assemblies in the broader context of the capsid lattice is lacking. In this study, we combined cryoelectron tomography and single particle analysis (SPA) cryoelectron microscopy to determine structures of continuous regions of the capsid lattice containing both hexamers and pentamers. We also developed a method of liposome scaffold-based in vitro lattice assembly ("lattice templating") that enabled us to directly study the lattice under a wider range of conditions than has previously been possible. Using this approach, we identified a critical role for inositol hexakisphosphate in pentamer formation and determined the structure of the CA lattice bound to the capsid-targeting antiretroviral drug GS-6207 (lenacapavir). Our work reveals key structural details of the mature HIV-1 CA lattice and establishes the combination of lattice templating and SPA as a robust strategy for studying retroviral capsid structure and capsid interactions with host proteins and antiviral compounds.
History
DepositionFeb 15, 2023-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateMay 10, 2023-
Current statusMay 10, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29777.png

Downloads & links

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Map

FileDownload / File: emd_29777.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 360 pix.
= 468. Å		1.3 Å/pix.
x 360 pix.
= 468. Å		1.3 Å/pix.
x 360 pix.
= 468. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0116
Minimum - Maximum-0.0054660295 - 0.027478531
Average (Standard dev.)0.00062608323 (±0.0021462715)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 467.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_29777_msk_1.map
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Half map: #1

Fileemd_29777_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_29777_half_map_2.map
Projections & Slices
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Sample components

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Entire : Defective HIV-1 capsid (CA) pentamer within surrounding hexameric...

EntireName: Defective HIV-1 capsid (CA) pentamer within surrounding hexameric CA lattice
Components
  • Complex: Defective HIV-1 capsid (CA) pentamer within surrounding hexameric CA lattice
    • Other: Capsid protein

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Supramolecule #1: Defective HIV-1 capsid (CA) pentamer within surrounding hexameric...

SupramoleculeName: Defective HIV-1 capsid (CA) pentamer within surrounding hexameric CA lattice
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Details: Partial HIV-1 capsid (CA) lattice assembled on small unilamellar vesicles at pH 7.4 in the absence of polyanionic assembly cofactor
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: other / ID: 1 / Classification: other
Source (natural)Organism: Human immunodeficiency virus 1
SequenceString: MPIVQNLQGQ MVHQAISPRT LNAWVKVVEE KAFSPEVIPM FSALSEGATP QDLNTMLNTV GGHQAAMQML KETINEEAAE WDRLHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT HNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE PFRDYVDRFY ...String:
MPIVQNLQGQ MVHQAISPRT LNAWVKVVEE KAFSPEVIPM FSALSEGATP QDLNTMLNTV GGHQAAMQML KETINEEAAE WDRLHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT HNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE PFRDYVDRFY KTLRAEQASQ EVKNWMTETL LVQNANPDCK TILKALGPGA TLEEMMTACQ GVGGPGHKAR VLHHHHHH
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

29772

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11558
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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