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- EMDB-15764: PDDC treatment HIV immature Gag -

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Basic information

Entry
Database: EMDB / ID: EMD-15764
TitlePDDC treatment HIV immature Gag
Map datamerged map
Sample
  • Virus: HIV-1 06TG.HT038 (virus)
KeywordsHIV / immature / gag / PDDC treatment / VIRUS LIKE PARTICLE
Biological speciesHIV-1 06TG.HT038 (virus)
Methodsubtomogram averaging / cryo EM / Resolution: 4.3 Å
AuthorsWaheed AA / Zhu Y / Agostino E / Naing L / Soheilian F / Song Y / Zhang P / Yoo S / Shlusher SB / Haughey N / Freed OE
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust206422/Z/17/Z United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Neutral sphingomyelinase 2 is required for HIV-1 maturation.
Authors: Abdul A Waheed / Yanan Zhu / Eva Agostino / Lwar Naing / Yuta Hikichi / Ferri Soheilian / Seung-Wan Yoo / Yun Song / Peijun Zhang / Barbara S Slusher / Norman J Haughey / Eric O Freed /
Abstract: HIV-1 assembly occurs at the inner leaflet of the plasma membrane (PM) in highly ordered membrane microdomains. The size and stability of membrane microdomains is regulated by activity of the ...HIV-1 assembly occurs at the inner leaflet of the plasma membrane (PM) in highly ordered membrane microdomains. The size and stability of membrane microdomains is regulated by activity of the sphingomyelin hydrolase neutral sphingomyelinase 2 (nSMase2) that is localized primarily to the inner leaflet of the PM. In this study, we demonstrate that pharmacological inhibition or depletion of nSMase2 in HIV-1-producer cells results in a block in the processing of the major viral structural polyprotein Gag and the production of morphologically aberrant, immature HIV-1 particles with severely impaired infectivity. We find that disruption of nSMase2 also severely inhibits the maturation and infectivity of other primate lentiviruses HIV-2 and simian immunodeficiency virus, has a modest or no effect on nonprimate lentiviruses equine infectious anemia virus and feline immunodeficiency virus, and has no effect on the gammaretrovirus murine leukemia virus. These studies demonstrate a key role for nSMase2 in HIV-1 particle morphogenesis and maturation.
History
DepositionSep 6, 2022-
Header (metadata) releaseMay 31, 2023-
Map releaseMay 31, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15764.png

Downloads & links

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Map

FileDownload / File: emd_15764.map.gz / Format: CCP4 / Size: 40.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmerged map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 219 pix.
= 293.46 Å		1.34 Å/pix.
x 219 pix.
= 293.46 Å		1.34 Å/pix.
x 219 pix.
= 293.46 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.68
Minimum - Maximum-6.5922937 - 14.046250000000001
Average (Standard dev.)0.045298066 (±0.56932235)
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: half2

Fileemd_15764_half_map_1.map
Annotationhalf2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half1

Fileemd_15764_half_map_2.map
Annotationhalf1
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.HT038

EntireName: HIV-1 06TG.HT038 (virus)
Components
  • Virus: HIV-1 06TG.HT038 (virus)

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Supramolecule #1: HIV-1 06TG.HT038

SupramoleculeName: HIV-1 06TG.HT038 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 587209 / Sci species name: HIV-1 06TG.HT038 / Virus type: VIRUS-LIKE PARTICLE / 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 stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 103350
ExtractionNumber tomograms: 43 / Number images used: 103350
Final angle assignmentType: ANGULAR RECONSTITUTION

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