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- EMDB-53086: Nuclear ring structure of the NPC of CEM cells -

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Basic information

Entry
Database: EMDB / ID: EMD-53086
TitleNuclear ring structure of the NPC of CEM cells
Map data
Sample
  • Complex: CEM T lymphoblast
KeywordsCA / subtomogram averaging / 6-fold symmetry / in situ / nuclear import / VIRAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 36.5 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: Nat Microbiol / Year: 2025
Title: HIV-1 nuclear import is selective and depends on both capsid elasticity and nuclear pore adaptability.
Authors: Zhen Hou / Yao Shen / Stanley Fronik / Juan Shen / Jiong Shi / Jialu Xu / Long Chen / Nathan Hardenbrook / Alan N Engelman / Christopher Aiken / Peijun Zhang /
Abstract: Lentiviruses, such as HIV-1, infect non-dividing cells by traversing the nuclear pore complex (NPC); however, the detailed molecular processes remain unclear. Here we reconstituted functional HIV-1 ...Lentiviruses, such as HIV-1, infect non-dividing cells by traversing the nuclear pore complex (NPC); however, the detailed molecular processes remain unclear. Here we reconstituted functional HIV-1 nuclear import using permeabilized T cells and isolated HIV-1 cores, which significantly increases import events, and developed an integrated three-dimensional cryo-correlative workflow to specifically target and image 1,489 native HIV-1 cores at 4 distinct nuclear import stages using cryo-electron tomography. We found HIV-1 nuclear import depends on both capsid elasticity and nuclear pore adaptability. The NPC acts as a selective filter, preferentially importing smaller cores, while expanding and deforming to accommodate their passage. Brittle mutant cores fail to enter the NPC, while CPSF6-binding-deficient cores enter but stall within the NPC, leading to impaired nuclear import. This study uncovers the interplay between the HIV-1 core and the NPC and provides a framework to dissect HIV-1 nuclear import and downstream events, such as uncoating and integration.
History
DepositionMar 10, 2025-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53086.png

Downloads & links

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Map

FileDownload / File: emd_53086.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
7.6 Å/pix.
x 72 pix.
= 547.2 Å		7.6 Å/pix.
x 72 pix.
= 547.2 Å		7.6 Å/pix.
x 72 pix.
= 547.2 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 7.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.3
Minimum - Maximum-10.492635 - 20.297577
Average (Standard dev.)0.99718374 (±2.7466323)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions727272
Spacing727272
CellA=B=C: 547.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53086_msk_1.map
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AxesZYX

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Histogram

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Half map: #1

Fileemd_53086_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53086_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : CEM T lymphoblast

EntireName: CEM T lymphoblast
Components
  • Complex: CEM T lymphoblast

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Supramolecule #1: CEM T lymphoblast

SupramoleculeName: CEM T lymphoblast / type: complex / 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
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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 36.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 1121
ExtractionNumber tomograms: 54 / Number images used: 2000
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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