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- EMDB-52138: In situ human cytoplasmic ring subunit of nuclear pore complex (F... -

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Basic information

Entry
Database: EMDB / ID: EMD-52138
TitleIn situ human cytoplasmic ring subunit of nuclear pore complex (FIB-lamella data of mock infected macrophages)
Map dataCytoplasmic ring of NPC from mock-infected macrophages - masked
Sample
  • Cell: In situ human cytoplasmic ring subunit of nuclear pore complex (FIB-lamella data of mock infected macrophages)
KeywordsNuclear envelope / Nuclear pore / Nucleocytoplasmic transport / NPC / STRUCTURAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 27.9 Å
AuthorsKreysing JP / Welsch S / Turonova B / Beck M
Funding support Germany, 2 items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)240245660 Germany
CitationJournal: Cell / Year: 2025
Title: Passage of the HIV capsid cracks the nuclear pore.
Authors: Jan Philipp Kreysing / Maziar Heidari / Vojtech Zila / Sergio Cruz-León / Agnieszka Obarska-Kosinska / Vibor Laketa / Lara Rohleder / Sonja Welsch / Jürgen Köfinger / Beata Turoňová / ...Authors: Jan Philipp Kreysing / Maziar Heidari / Vojtech Zila / Sergio Cruz-León / Agnieszka Obarska-Kosinska / Vibor Laketa / Lara Rohleder / Sonja Welsch / Jürgen Köfinger / Beata Turoňová / Gerhard Hummer / Hans-Georg Kräusslich / Martin Beck /
Abstract: Upon infection, human immunodeficiency virus type 1 (HIV-1) releases its cone-shaped capsid into the cytoplasm of infected T cells and macrophages. The capsid enters the nuclear pore complex (NPC), ...Upon infection, human immunodeficiency virus type 1 (HIV-1) releases its cone-shaped capsid into the cytoplasm of infected T cells and macrophages. The capsid enters the nuclear pore complex (NPC), driven by interactions with numerous phenylalanine-glycine (FG)-repeat nucleoporins (FG-Nups). Whether NPCs structurally adapt to capsid passage and whether capsids are modified during passage remains unknown, however. Here, we combined super-resolution and correlative microscopy with cryoelectron tomography and molecular simulations to study the nuclear entry of HIV-1 capsids in primary human macrophages. Our data indicate that cytosolically bound cyclophilin A is stripped off capsids entering the NPC, and the capsid hexagonal lattice remains largely intact inside and beyond the central channel. Strikingly, the NPC scaffold rings frequently crack during capsid passage, consistent with computer simulations indicating the need for NPC widening. The unique cone shape of the HIV-1 capsid facilitates its entry into NPCs and helps to crack their rings.
History
DepositionNov 19, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52138.png

Downloads & links

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Map

FileDownload / File: emd_52138.map.gz / Format: CCP4 / Size: 5.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCytoplasmic ring of NPC from mock-infected macrophages - masked
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
9.66 Å/pix.
x 112 pix.
= 1081.472 Å		9.66 Å/pix.
x 112 pix.
= 1081.472 Å		9.66 Å/pix.
x 112 pix.
= 1081.472 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 9.656 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.57713765 - 0.77081233
Average (Standard dev.)0.0001871593 (±0.028217712)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions112112112
Spacing112112112
CellA=B=C: 1081.472 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Cytoplasmic ring of NPC from mock-infected macrophages - unmasked

Fileemd_52138_additional_1.map
AnnotationCytoplasmic ring of NPC from mock-infected macrophages - unmasked
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cytoplasmic ring of NPC from mock-infected macrophages - half1

Fileemd_52138_half_map_1.map
AnnotationCytoplasmic ring of NPC from mock-infected macrophages - half1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cytoplasmic ring of NPC from mock-infected macrophages - half2

Fileemd_52138_half_map_2.map
AnnotationCytoplasmic ring of NPC from mock-infected macrophages - half2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : In situ human cytoplasmic ring subunit of nuclear pore complex (F...

EntireName: In situ human cytoplasmic ring subunit of nuclear pore complex (FIB-lamella data of mock infected macrophages)
Components
  • Cell: In situ human cytoplasmic ring subunit of nuclear pore complex (FIB-lamella data of mock infected macrophages)

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Supramolecule #1: In situ human cytoplasmic ring subunit of nuclear pore complex (F...

SupramoleculeName: In situ human cytoplasmic ring subunit of nuclear pore complex (FIB-lamella data of mock infected macrophages)
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: 7.4
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber temperature: 310 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 2.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 53000
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: 27.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: novaSTA / Number subtomograms used: 721
ExtractionNumber tomograms: 52 / Number images used: 940 / Software - Name: novaSTA
Final angle assignmentType: OTHER / Software - Name: novaSTA / Details: Cross correlations
FSC plot (resolution estimation)

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