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- EMDB-53085: Luminal ring structure of the NPC of CEM cells -

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Basic information

Entry
Database: EMDB / ID: EMD-53085
TitleLuminal 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: 32.1 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
DepositionMar 10, 2025-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53085.png

Downloads & links

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Map

FileDownload / File: emd_53085.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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 7.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.24
Minimum - Maximum-26.264876999999998 - 33.884540000000001
Average (Standard dev.)1.4150578 (±3.8260217)
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_53085_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_53085_half_map_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #2

Fileemd_53085_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: 32.1 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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