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- EMDB-51466: HIV-1 Nuclear Condensate under NEV treatment -

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Basic information

Entry
Database: EMDB / ID: EMD-51466
TitleHIV-1 Nuclear Condensate under NEV treatment
Map dataNuclear HIV-CPSF6 site in infected cells treated with NEV
Sample
  • Cell: THP-1 cells infected with HIV-1 and treated with Nevirapine (NEV)
KeywordsHIV-1 nuclear condensates / CPSF6 / Capsid / Nevirapine / immuno-gold 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_51466.png

Downloads & links

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Map

FileDownload / File: emd_51466.map.gz / Format: CCP4 / Size: 2.5 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationNuclear HIV-CPSF6 site in infected cells treated with NEV
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.03 Å/pix.
x 109 pix.
= 439.488 Å		4.03 Å/pix.
x 3440 pix.
= 13870.08 Å		4.03 Å/pix.
x 3604 pix.
= 14531.328 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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 - 3164.0
Average (Standard dev.)792.895449999999983 (±125.553550000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions34403604109
Spacing36043440109
CellA: 14531.328 Å / B: 13870.08 Å / C: 439.488 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Manually annotated Dense HIV cores

Fileemd_51466_additional_1.map
AnnotationManually annotated Dense HIV cores
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram (log scale)

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Additional map: Manually Annotated Lighter HIV Cores

Fileemd_51466_additional_2.map
AnnotationManually Annotated Lighter HIV Cores
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: Manually Annotated Ghost HIV Cores

Fileemd_51466_additional_3.map
AnnotationManually Annotated Ghost HIV Cores
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : THP-1 cells infected with HIV-1 and treated with Nevirapine (NEV)

EntireName: THP-1 cells infected with HIV-1 and treated with Nevirapine (NEV)
Components
  • Cell: THP-1 cells infected with HIV-1 and treated with Nevirapine (NEV)

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Supramolecule #1: THP-1 cells infected with HIV-1 and treated with Nevirapine (NEV)

SupramoleculeName: THP-1 cells infected with HIV-1 and treated with Nevirapine (NEV)
type: cell / ID: 1 / Parent: 0
Details: Double immunolabelled Tokuyasu style sections of HIV infected cells. HIV cores found in an CPSF6 nuclear condensate (10nm immunogold targets CPSF6, 6nm gold the HIV capsid protein)
Source (natural)Organism: HIV-1 vector pNL4-3 (others)

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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
DetailsInfected cells were sectioned using the Tokuyasu protocol and immunolabelled against CPSF6 (10nm beads) and capsid protein (6nm beads)
SectioningUltramicrotomy - Instrument: Leica EM UC7 / Ultramicrotomy - Temperature: 153 K / Ultramicrotomy - Final thickness: 80

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Electron microscopy

MicroscopeJEOL 1400
DetailsClassical TEM imaging using contrasting agent. Preliminary grid screening performed manually.
Image recordingFilm or detector model: OTHER / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 230 / Average electron dose: 200.0 e/Å2
Details: Classical TEM imaging under high dose conditions. Prior data acquisition mild cooking took place in middle magnifications.
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

DetailsGatan ONeView
Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD
Details: Back projection in IMOD using the SIRT-like filter (12 iterations) of axes A and B.
Number images used: 230

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