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- EMDB-52144: In situ human symmetrized composite map of nuclear pore complex (... -

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Basic information

Entry
Database: EMDB / ID: EMD-52144
TitleIn situ human symmetrized composite map of nuclear pore complex (FIB-lamella data of mock infected macrophages)
Map dataIn situ human symmetrized composite map of NPC from mock infected macrophages
Sample
  • Cell: In situ human composite map of nuclear pore complex (FIB-lamella data of mock infected macrophages)
KeywordsNuclear envelope / Nuclear pore / Nucleocytoplasmic transport / NPC / STRUCTURAL PROTEIN / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 30.0 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-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52144.png

Downloads & links

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Map

FileDownload / File: emd_52144.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIn situ human symmetrized composite map of NPC from mock infected macrophages
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
9.66 Å/pix.
x 192 pix.
= 1853.952 Å		9.66 Å/pix.
x 192 pix.
= 1853.952 Å		9.66 Å/pix.
x 192 pix.
= 1853.952 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: 0.06
Minimum - Maximum-0.5396986 - 0.91195506
Average (Standard dev.)0.006265617 (±0.045543633)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 1853.952 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : In situ human composite map of nuclear pore complex (FIB-lamella ...

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

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Supramolecule #1: In situ human composite map of nuclear pore complex (FIB-lamella ...

SupramoleculeName: In situ human composite map 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: C8 (8 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: OTHER / Software - Name: novaSTA / Number subtomograms used: 760
ExtractionNumber tomograms: 52 / Number images used: 940 / Software - Name: novaSTA
Final angle assignmentType: OTHER / Software - Name: novaSTA / Details: Cross correlations

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