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- EMDB-51630: In situ human basket attachment to nuclear ring of nuclear pore c... -

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Basic information

Entry
Database: EMDB / ID: EMD-51630
TitleIn situ human basket attachment to nuclear ring of nuclear pore complex (FIB-lamella data of HIV infected macrophages)
Map dataBasket attachment to nuclear ring of NPC from HIV-infected macrophages - masked
Sample
  • Cell: In situ human basket attachment to nuclear ring of nuclear pore complex (FIB-lamella data of HIV infected macrophages)
KeywordsNuclear envelope / Nuclear pore / Nucleocytoplasmic transport / NPC / STRUCTURAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 33.2 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
DepositionSep 23, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51630.png

Downloads & links

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Map

FileDownload / File: emd_51630.map.gz / Format: CCP4 / Size: 5.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBasket attachment to nuclear ring of NPC from HIV-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: 0.08
Minimum - Maximum-0.38099036 - 0.588241
Average (Standard dev.)-0.00042225354 (±0.009572833)
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: Basket attachment to nuclear ring of NPC from...

Fileemd_51630_additional_1.map
AnnotationBasket attachment to nuclear ring of NPC from HIV-infected macrophages - unmasked
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Basket attachment to nuclear ring of NPC from...

Fileemd_51630_half_map_1.map
AnnotationBasket attachment to nuclear ring of NPC from HIV-infected macrophages - half1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Basket attachment to nuclear ring of NPC from...

Fileemd_51630_half_map_2.map
AnnotationBasket attachment to nuclear ring of NPC from HIV-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 basket attachment to nuclear ring of nuclear pore c...

EntireName: In situ human basket attachment to nuclear ring of nuclear pore complex (FIB-lamella data of HIV infected macrophages)
Components
  • Cell: In situ human basket attachment to nuclear ring of nuclear pore complex (FIB-lamella data of HIV infected macrophages)

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Supramolecule #1: In situ human basket attachment to nuclear ring of nuclear pore c...

SupramoleculeName: In situ human basket attachment to nuclear ring of nuclear pore complex (FIB-lamella data of HIV 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: 33.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: novaSTA / Number subtomograms used: 1044
ExtractionNumber tomograms: 97 / Number images used: 1600 / Software - Name: novaSTA
Final angle assignmentType: OTHER / Software - Name: novaSTA / Details: Cross correlations
FSC plot (resolution estimation)

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