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- EMDB-53458: In situ cryo-EM structure of HIV-1 VLP CA hexamer before the nucl... -

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Basic information

Entry
Database: EMDB / ID: EMD-53458
TitleIn situ cryo-EM structure of HIV-1 VLP CA hexamer before the nuclear import
Map data
Sample
  • Cell: Permeabilised CEM cell incubated with purified HIV-1 VLP cores
KeywordsComplex / VIRAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 12.5 Å
AuthorsHou Z / Chen L / Zhang P
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust206422/Z/17/Z United Kingdom
CitationJournal: EMBO Rep / Year: 2025
Title: Direct visualization of HIV-1 core nuclear import and its interplay with the nuclear pore.
Authors: Zhen Hou / Stanley Fronik / Yao Shen / Long Chen / Christopher Thompson / Sarah Neumann / Peijun Zhang /
Abstract: Direct visualization of HIV-1 nuclear import through the nuclear pore complex (NPC) presents a technical challenge due to the rarity of this process. To enable systematic investigation, we developed ...Direct visualization of HIV-1 nuclear import through the nuclear pore complex (NPC) presents a technical challenge due to the rarity of this process. To enable systematic investigation, we developed a robust in situ system that mimics HIV-1 nuclear import in a near-native context using isolated HIV-1 virus like particles (VLP) cores and permeabilized CD4 + T lymphocyte (CEM) cells. This approach supports docking and translocation of abundant viral cores through nuclear pores into the nucleus. For high-resolution visualization, we implemented an integrated correlative approach to guide cryo-focused ion beam (cryo-FIB) milling and cryo-electron tomography (cryo-ET) imaging, enabling precise targeting and structural characterization of individual nuclear import events. Using this workflow, we visualized 510 HIV-1 VLP cores at distinct stages of nuclear import, capturing key snapshots of the full progression of nuclear import. Subsequent statistical and structural analyses allow classification of core morphologies and identification of translocation-associated remodeling in nuclear pores. This work provides a methodological foundation for dissecting HIV-1 and potentially other viruses nuclear import processes and post-entry events in a controlled and quantitative manner.
History
DepositionApr 19, 2025-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53458.png

Downloads & links

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Map

FileDownload / File: emd_53458.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
3.8 Å/pix.
x 96 pix.
= 364.8 Å		3.8 Å/pix.
x 96 pix.
= 364.8 Å		3.8 Å/pix.
x 96 pix.
= 364.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 3.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.88
Minimum - Maximum-1.9531337 - 8.347451
Average (Standard dev.)0.10223488 (±0.5937148)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 364.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_53458_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53458_half_map_2.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 : Permeabilised CEM cell incubated with purified HIV-1 VLP cores

EntireName: Permeabilised CEM cell incubated with purified HIV-1 VLP cores
Components
  • Cell: Permeabilised CEM cell incubated with purified HIV-1 VLP cores

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Supramolecule #1: Permeabilised CEM cell incubated with purified HIV-1 VLP cores

SupramoleculeName: Permeabilised CEM cell incubated with purified HIV-1 VLP cores
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 77.0 K
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 2.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 64000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: 12.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1222
ExtractionNumber tomograms: 7 / Number images used: 3500
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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