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- EMDB-52888: In-situ structure of HIV-1 CA hexamer before the nuclear import -

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Entry
Database: EMDB / ID: EMD-52888
TitleIn-situ structure of HIV-1 CA hexamer before the nuclear import
Map dataIn-situ structure of HIV-1 CA hexamer before the nuclear import
Sample
  • Complex: HIV-1 CA protein hexamer
KeywordsCA / subtomogram averaging / 6-fold symmetry / in situ / nuclear import / VIRAL PROTEIN
Biological speciesHIV-1 (virus)
Methodsubtomogram averaging / cryo EM / Resolution: 11.05 Å
AuthorsHou Z / Zhang P / Shen Y / Fronik S / Shen J / Shi J / Xu J / Chen L / Hardenbrook N / Thompson C ...Hou Z / Zhang P / Shen Y / Fronik S / Shen J / Shi J / Xu J / Chen L / Hardenbrook N / Thompson C / Neumann S / Engelman A / Aiken C
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust203141/Z/16/Z United Kingdom
CitationJournal: bioRxiv / Year: 2025
Title: Correlative In Situ Cryo-ET Reveals Cellular and Viral Remodeling Associated with Selective HIV-1 Core Nuclear Import.
Authors: Zhen Hou / Yao Shen / Stanley Fronik / Juan Shen / Jiong Shi / Jialu Xu / Long Chen / Nathan Hardenbrook / Christopher Thompson / Sarah Neumann / Alan N Engelman / Christopher Aiken / Peijun Zhang /
Abstract: Lentiviruses like HIV-1 infect non-dividing cells by traversing the nuclear pore, but studying this process has been challenging due to its scarcity and dynamic nature in infected cells. Here, we ...Lentiviruses like HIV-1 infect non-dividing cells by traversing the nuclear pore, but studying this process has been challenging due to its scarcity and dynamic nature in infected cells. Here, we developed a robust cell-permeabilization system that recapitulates HIV-1 nuclear import and established an integrated cryo-correlative workflow combining cryo-CLEM, cryo-FIB, and cryo-ET for targeted imaging of this process. These advancements enabled the successful capture of 1,899 HIV-1 cores at various stages of nuclear import. Statistical and structural analyses of native wild-type and mutant cores revealed that HIV-1 nuclear import depends on both capsid elasticity and nuclear pore adaptability, as well as nuclear factors such as CPSF6. Brittle cores fail to enter the nuclear pore complex (NPC), while CPSF6-binding-deficient cores stall inside the NPC, resulting in impaired nuclear import. Intriguingly, nuclear pores function as selective filters favoring the import of smaller, tube-shaped cores. Our study opens new avenues for dissecting the biochemistry and structural biology of HIV-1 nuclear import as well as downstream events including core uncoating and potentially integration, with unprecedented detail.
History
DepositionFeb 22, 2025-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52888.png

Downloads & links

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Map

FileDownload / File: emd_52888.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIn-situ structure of HIV-1 CA hexamer before the nuclear import
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 13.91
Minimum - Maximum-22.261548999999999 - 61.757579999999997
Average (Standard dev.)0.59660673 (±4.4606633)
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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Mask #1

Fileemd_52888_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: Half map1

Fileemd_52888_half_map_1.map
AnnotationHalf map1
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map2

Fileemd_52888_half_map_2.map
AnnotationHalf map2
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : HIV-1 CA protein hexamer

EntireName: HIV-1 CA protein hexamer
Components
  • Complex: HIV-1 CA protein hexamer

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Supramolecule #1: HIV-1 CA protein hexamer

SupramoleculeName: HIV-1 CA protein hexamer / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: HIV-1 (virus)

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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-PROPANE
DetailsHIV-1 capsids were incubated with permeabilised CEM cell

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / 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 defocus max: 5.5 µm / Calibrated defocus min: 2.7 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 64000
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: 11.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 11915
ExtractionNumber tomograms: 128 / Number images used: 2000
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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