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- EMDB-53458: In situ cryo-EM structure of HIV-1 VLP CA hexamer before the nucl... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-53458
TitleIn situ cryo-EM structure of HIV-1 VLP CA hexamer before the nuclear import
Map data
Sample
  • Cell: Permeabilised CEM cell incubated with purified HIV-1 VLP cores
KeywordsComplex / VIRAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 12.5 Å
AuthorsHou Z / Chen L / Zhang PJ
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust206422/Z/17/Z United Kingdom
CitationJournal: To Be Published
Title: Direct visualisation of HIV-1 nuclear import
Authors: Hou Z / Fronik S / Shen Y / Chen L / Thompson C / Neumann S / Zhang PJ
History
DepositionApr 19, 2025-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53458.png

Downloads & links

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Map

FileDownload / File: emd_53458.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.8 Å/pix.
x 96 pix.
= 364.8 Å		3.8 Å/pix.
x 96 pix.
= 364.8 Å		3.8 Å/pix.
x 96 pix.
= 364.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.88
Minimum - Maximum-1.9531337 - 8.347451
Average (Standard dev.)0.10223488 (±0.5937148)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 364.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_53458_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53458_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Permeabilised CEM cell incubated with purified HIV-1 VLP cores

EntireName: Permeabilised CEM cell incubated with purified HIV-1 VLP cores
Components
  • Cell: Permeabilised CEM cell incubated with purified HIV-1 VLP cores

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Supramolecule #1: Permeabilised CEM cell incubated with purified HIV-1 VLP cores

SupramoleculeName: Permeabilised CEM cell incubated with purified HIV-1 VLP cores
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
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 77.0 K
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 2.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 64000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: 12.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1222
ExtractionNumber tomograms: 7 / Number images used: 3500
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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