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- EMDB-11967: Human nuclear pore complex in HIV-1 infected T cells -

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Basic information

Entry
Database: EMDB / ID: EMD-11967
TitleHuman nuclear pore complex in HIV-1 infected T cells
Map dataHuman Nuclear Pore Complex from HIV-1 infected T cells
Sample
  • Complex: Nuclear pore complex from HIV-1 infected T cells
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 37.0 Å
AuthorsMargiotta E / Beck M
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
Citation
Journal: Cell / Year: 2021
Title: Cone-shaped HIV-1 capsids are transported through intact nuclear pores.
Authors: Vojtech Zila / Erica Margiotta / Beata Turoňová / Thorsten G Müller / Christian E Zimmerli / Simone Mattei / Matteo Allegretti / Kathleen Börner / Jona Rada / Barbara Müller / Marina ...Authors: Vojtech Zila / Erica Margiotta / Beata Turoňová / Thorsten G Müller / Christian E Zimmerli / Simone Mattei / Matteo Allegretti / Kathleen Börner / Jona Rada / Barbara Müller / Marina Lusic / Hans-Georg Kräusslich / Martin Beck /
Abstract: Human immunodeficiency virus (HIV-1) remains a major health threat. Viral capsid uncoating and nuclear import of the viral genome are critical for productive infection. The size of the HIV-1 capsid ...Human immunodeficiency virus (HIV-1) remains a major health threat. Viral capsid uncoating and nuclear import of the viral genome are critical for productive infection. The size of the HIV-1 capsid is generally believed to exceed the diameter of the nuclear pore complex (NPC), indicating that capsid uncoating has to occur prior to nuclear import. Here, we combined correlative light and electron microscopy with subtomogram averaging to capture the structural status of reverse transcription-competent HIV-1 complexes in infected T cells. We demonstrated that the diameter of the NPC in cellulo is sufficient for the import of apparently intact, cone-shaped capsids. Subsequent to nuclear import, we detected disrupted and empty capsid fragments, indicating that uncoating of the replication complex occurs by breaking the capsid open, and not by disassembly into individual subunits. Our data directly visualize a key step in HIV-1 replication and enhance our mechanistic understanding of the viral life cycle.
#1: Journal: To Be Published
Title: Cone-shaped HIV-1 capsids are transported through intact nuclear pores
Authors: Zila V / Margiotta E
History
DepositionNov 20, 2020-
Header (metadata) releaseFeb 17, 2021-
Map releaseFeb 17, 2021-
UpdateMar 3, 2021-
Current statusMar 3, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11967.png

Downloads & links

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Map

FileDownload / File: emd_11967.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman Nuclear Pore Complex from HIV-1 infected T cells
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
13.8 Å/pix.
x 144 pix.
= 1987.2 Å		13.8 Å/pix.
x 144 pix.
= 1987.2 Å		13.8 Å/pix.
x 144 pix.
= 1987.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 13.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.30114084 - 0.52442425
Average (Standard dev.)0.002434907 (±0.035874195)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions144144144
Spacing144144144
CellA=B=C: 1987.2001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z13.813.813.8
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z1987.2001987.2001987.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS144144144
D min/max/mean-0.3010.5240.002

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Supplemental data

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Sample components

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Entire : Nuclear pore complex from HIV-1 infected T cells

EntireName: Nuclear pore complex from HIV-1 infected T cells
Components
  • Complex: Nuclear pore complex from HIV-1 infected T cells

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Supramolecule #1: Nuclear pore complex from HIV-1 infected T cells

SupramoleculeName: Nuclear pore complex from HIV-1 infected T cells / 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: 7.4 / Details: RPMI 1640 medium with GlutaMAX
GridModel: Quantifoil / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 310.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 4.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 42000
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: 37.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 90
ExtractionNumber tomograms: 250 / Number images used: 99
CTF correctionDetails: novaCTF (Turonova et al., 2017)
Final angle assignmentType: PROJECTION MATCHING

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