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- EMDB-51532: HIV-1 CA hexamer from cytoplasmic capsids (FIB-lamella data of HI... -

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Basic information

Entry
Database: EMDB / ID: EMD-51532
TitleHIV-1 CA hexamer from cytoplasmic capsids (FIB-lamella data of HIV infected macrophages)
Map dataHIV CA hexamer from cytoplasmic capsids - main map
Sample
  • Virus: Human immunodeficiency virus type 1, NNHIV
KeywordsHIV / HIV-1 / CA hexamer / capsid / FIB-SEM / lamella / cryo-ET / STA / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus type 1, NNHIV
Methodsubtomogram averaging / cryo EM / Resolution: 27.7 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 13, 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_51532.png

Downloads & links

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Map

FileDownload / File: emd_51532.map.gz / Format: CCP4 / Size: 2.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV CA hexamer from cytoplasmic capsids - main map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.83 Å/pix.
x 84 pix.
= 405.552 Å		4.83 Å/pix.
x 84 pix.
= 405.552 Å		4.83 Å/pix.
x 84 pix.
= 405.552 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.5204959 - 0.5065095
Average (Standard dev.)0.0028762422 (±0.04510129)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions848484
Spacing848484
CellA=B=C: 405.552 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: HIV CA hexamer from cytoplasmic capsids - halfmap 2

Fileemd_51532_half_map_1.map
AnnotationHIV CA hexamer from cytoplasmic capsids - halfmap 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HIV CA hexamer from cytoplasmic capsids - halfmap 1

Fileemd_51532_half_map_2.map
AnnotationHIV CA hexamer from cytoplasmic capsids - halfmap 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human immunodeficiency virus type 1, NNHIV

EntireName: Human immunodeficiency virus type 1, NNHIV
Components
  • Virus: Human immunodeficiency virus type 1, NNHIV

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Supramolecule #1: Human immunodeficiency virus type 1, NNHIV

SupramoleculeName: Human immunodeficiency virus type 1, NNHIV / type: virus / ID: 1 / Parent: 0
Details: For production of non-infectious IN.mScarlet labeled R5-tropic NNHIV, HEK293T cells were transfected with pNNHIVdeltaEnv, 490 pVpr.INNN.mScarlet and pEnv-4059 at a molar ratio of 4.5:1:1.
NCBI-ID: 11676
Sci species name: Human immunodeficiency virus type 1, NNHIV
Sci species strain: NL4-3 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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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: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 27.7 Å / Resolution method: FSC 0.5 CUT-OFF
Software:
Namedetails
novaSTA
RELION (ver. 3.1)for postprocessing only

Number subtomograms used: 1675
ExtractionNumber tomograms: 11 / Number images used: 89017 / Method: Surface oversampling / Software - Name: novaSTA
Final angle assignmentType: OTHER / Software - Name: novaSTA / Details: Cross correlations
FSC plot (resolution estimation)

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