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- EMDB-51462: Nuclear HIV-1 Condensate -

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Basic information

Entry
Database: EMDB / ID: EMD-51462
TitleNuclear HIV-1 Condensate
Map dataNuclear HIV1 condensates
Sample
  • Cell: THP1 cells infected with HIV-1
KeywordsHIV-1 MembraneLess Organelles / Nuclear condensates / CPSF6 / Capsid / immunogold labelling / VIRUS
Biological speciesHIV-1 vector pNL4-3 (others)
Methodelectron tomography / negative staining
AuthorsGazi AD / Burlaud-Gaillard J / Roingeard P / Di Nunzio F
Funding support France, 2 items
OrganizationGrant numberCountry
Agence Nationale de Recherches Sur le Sida et les Hepatites Virales (ANRS)ECTZ192036 France
Agence Nationale de Recherches Sur le Sida et les Hepatites Virales (ANRS)ECTZ137593 France
CitationJournal: EMBO J / Year: 2025
Title: In vivo HIV-1 nuclear condensates safeguard against cGAS and license reverse transcription.
Authors: Selen Ay / Julien Burlaud-Gaillard / Anastasia Gazi / Yevgeniy Tatirovsky / Celine Cuche / Jean-Sebastien Diana / Viviana Scoca / James P Di Santo / Philippe Roingeard / Fabrizio Mammano / Francesca Di Nunzio /
Abstract: Entry of viral capsids into the nucleus induces the formation of biomolecular condensates called HIV-1 membraneless organelles (HIV-1-MLOs). Several questions remain about their persistence, in vivo ...Entry of viral capsids into the nucleus induces the formation of biomolecular condensates called HIV-1 membraneless organelles (HIV-1-MLOs). Several questions remain about their persistence, in vivo formation, composition, and function. Our study reveals that HIV-1-MLOs persisted for several weeks in infected cells, and their abundance correlated with viral infectivity. Using an appropriate animal model, we show that HIV-1-MLOs were formed in vivo during acute infection. To explore the viral structures present within these biomolecular condensates, we used a combination of double immunogold labeling, electron microscopy and tomography, and unveiled a diverse array of viral core structures. Our functional analyses showed that HIV-1-MLOs remained stable during treatment with a reverse transcriptase inhibitor, maintaining the virus in a dormant state. Drug withdrawal restored reverse transcription, promoting efficient virus replication akin to that observed in latently infected patients on antiretroviral therapy. However, when HIV-1 MLOs were deliberately disassembled by pharmacological treatment, we observed a complete loss of viral infectivity. Our findings show that HIV-1 MLOs shield the final reverse transcription product from host immune detection.
History
DepositionSep 2, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51462.png

Downloads & links

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Map

FileDownload / File: emd_51462.map.gz / Format: CCP4 / Size: 2.2 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationNuclear HIV1 condensates
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
4.03 Å/pix.
x 104 pix.
= 419.328 Å		4.03 Å/pix.
x 3005 pix.
= 12116.16 Å		4.03 Å/pix.
x 3707 pix.
= 14946.624 Å

Projections

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Slices (1/2)

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Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 4.032 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum0.0 - 1496.0
Average (Standard dev.)553.085900000000038 (±85.458659999999995)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions30053707104
Spacing37073005104
CellA: 14946.624 Å / B: 12116.16 Å / C: 419.328 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Manual annotation of Dense HIV Cores

Fileemd_51462_additional_1.map
AnnotationManual annotation of Dense HIV Cores
Projections & Slices
AxesZYX

Projections

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Histogram

Histogram (log scale)

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Additional map: Manual annotation of HIV ghosts

Fileemd_51462_additional_2.map
AnnotationManual annotation of HIV ghosts
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: Manual annotation of Lighter HIV Cores

Fileemd_51462_additional_3.map
AnnotationManual annotation of Lighter HIV Cores
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : THP1 cells infected with HIV-1

EntireName: THP1 cells infected with HIV-1
Components
  • Cell: THP1 cells infected with HIV-1

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Supramolecule #1: THP1 cells infected with HIV-1

SupramoleculeName: THP1 cells infected with HIV-1 / type: cell / ID: 1 / Parent: 0
Details: Double immunolabelled Tokuyasu-like section of HIV infected cells: HIV capsids are found in a nuclear CPSF6 condensate (labelled with 10nm immunogold, while CA protein is also labeled with 6nm immunogold).
Source (natural)Organism: HIV-1 vector pNL4-3 (others) / Strain: THP-1 (ATCC Number: TIB-202)

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Experimental details

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Structure determination

Methodnegative staining
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.6
StainingType: NEGATIVE / Material: 2% Uranyl Acetate
GridMaterial: NICKEL
DetailsCells were sectioned using the Tokuyasu protocol and immunolabelled with anti-CPSF6 (using goat-anti-rabbit 10nm gold bead conjugated as a secondary antibody) and anti-P24 (using goat-anti-mouse 6nm gold bead conjugated antibody).
SectioningUltramicrotomy - Instrument: Leica EM UC7 / Ultramicrotomy - Temperature: 153 K / Ultramicrotomy - Final thickness: 80

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Electron microscopy

MicroscopeJEOL 1400
DetailsClassical TEM imaging (Room Temperature). Preliminary grid screening was performed manually.
Image recordingFilm or detector model: OTHER / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 200.0 e/Å2
Details: Classical TEM imaging under high dose condtions with mild cooking in lower magnification. All focusing and tracking steps during tilt series acquisitions took place at the same area.
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC

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Image processing

DetailsThe detector used for tilt series acquisition was the GATAN-OneView
Final reconstructionAlgorithm: BACK PROJECTION / Resolution method: OTHER / Software - Name: IMOD / Details: This is a dual-axis tomogram. / Number images used: 230

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