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- EMDB-16187: Wild tye immature Gag Structure -

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Basic information

Entry
Database: EMDB / ID: EMD-16187
TitleWild tye immature Gag Structure
Map datamerged map
Sample
  • Virus: HIV-1 06TG.HT008 (virus)
KeywordsHIV-1 / Immature Gag / Wild type / VIRUS LIKE PARTICLE
Biological speciesHIV-1 06TG.HT008 (virus)
Methodsubtomogram averaging / cryo EM / Resolution: 4.15 Å
AuthorsZhu Y / Chen L / Hardenbrook N / Zhang P
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: J Mol Biol / Year: 2023
Title: The Effect of Inositol Hexakisphosphate on HIV-1 Particle Production and Infectivity can be Modulated by Mutations that Affect the Stability of the Immature Gag Lattice.
Authors: Alex B Kleinpeter / Yanan Zhu / Donna L Mallery / Sherimay D Ablan / Long Chen / Nathan Hardenbrook / Adolfo Saiardi / Leo C James / Peijun Zhang / Eric O Freed /
Abstract: The assembly of an HIV-1 particle begins with the construction of a spherical lattice composed of hexamer subunits of the Gag polyprotein. The cellular metabolite inositol hexakisphosphate (IP6) ...The assembly of an HIV-1 particle begins with the construction of a spherical lattice composed of hexamer subunits of the Gag polyprotein. The cellular metabolite inositol hexakisphosphate (IP6) binds and stabilizes the immature Gag lattice via an interaction with the six-helix bundle (6HB), a crucial structural feature of Gag hexamers that modulates both virus assembly and infectivity. The 6HB must be stable enough to promote immature Gag lattice formation, but also flexible enough to be accessible to the viral protease, which cleaves the 6HB during particle maturation. 6HB cleavage liberates the capsid (CA) domain of Gag from the adjacent spacer peptide 1 (SP1) and IP6 from its binding site. This pool of IP6 molecules then promotes the assembly of CA into the mature conical capsid that is required for infection. Depletion of IP6 in virus-producer cells results in severe defects in assembly and infectivity of wild-type (WT) virions. Here we show that in an SP1 double mutant (M4L/T8I) with a hyperstable 6HB, IP6 can block virion infectivity by preventing CA-SP1 processing. Thus, depletion of IP6 in virus-producer cells markedly increases M4L/T8I CA-SP1 processing and infectivity. We also show that the introduction of the M4L/T8I mutations partially rescues the assembly and infectivity defects induced by IP6 depletion on WT virions, likely by increasing the affinity of the immature lattice for limiting IP6. These findings reinforce the importance of the 6HB in virus assembly, maturation, and infection and highlight the ability of IP6 to modulate 6HB stability.
History
DepositionNov 21, 2022-
Header (metadata) releaseJul 5, 2023-
Map releaseJul 5, 2023-
UpdateNov 1, 2023-
Current statusNov 1, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16187.png

Downloads & links

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Map

FileDownload / File: emd_16187.map.gz / Format: CCP4 / Size: 40.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmerged map
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 2.93
Minimum - Maximum-4.9944487 - 11.5662565
Average (Standard dev.)0.05650698 (±0.56058025)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions219219219
Spacing219219219
CellA=B=C: 293.46002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map

Fileemd_16187_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_16187_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HIV-1 06TG.HT008

EntireName: HIV-1 06TG.HT008 (virus)
Components
  • Virus: HIV-1 06TG.HT008 (virus)

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Supramolecule #1: HIV-1 06TG.HT008

SupramoleculeName: HIV-1 06TG.HT008 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 587638 / Sci species name: HIV-1 06TG.HT008 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 41 / Number images used: 114401
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 114401

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