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- EMDB-51740: Subtomogram average of nuclear helical M1 assemblies -

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Basic information

Entry
Database: EMDB / ID: EMD-51740
TitleSubtomogram average of nuclear helical M1 assemblies
Map dataSubtomogram average of nuclear helical M1 assemblies
Sample
  • Cell: A549wt cell infected with PR8 virus at 16 hpi.
KeywordsInfluenza A virus / VIRUS
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 34.0 Å
AuthorsWachsmuth-Melm M / Chlanda P
Funding support Germany, 3 items
OrganizationGrant numberCountry
Other privateChica and Heinz Schaller Foundation
German Research Foundation (DFG)437060729 Germany
German Research Foundation (DFG)240245660 Germany
CitationJournal: To Be Published
Title: Influenza A virus hemagglutinin remodels membranes into a vRNP clustering platform
Authors: Wachsmuth-Melm M / Chlanda P / Peterl S / Makroczyova J / Vale-Costa S / Amorim MJ
History
DepositionOct 8, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51740.png

Downloads & links

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Map

FileDownload / File: emd_51740.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of nuclear helical M1 assemblies
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.18 Å/pix.
x 192 pix.
= 994.176 Å		5.18 Å/pix.
x 192 pix.
= 994.176 Å		5.18 Å/pix.
x 192 pix.
= 994.176 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.178 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.030758068 - 0.08976259
Average (Standard dev.)0.005417746 (±0.018530982)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 994.176 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_51740_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51740_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 : A549wt cell infected with PR8 virus at 16 hpi.

EntireName: A549wt cell infected with PR8 virus at 16 hpi.
Components
  • Cell: A549wt cell infected with PR8 virus at 16 hpi.

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Supramolecule #1: A549wt cell infected with PR8 virus at 16 hpi.

SupramoleculeName: A549wt cell infected with PR8 virus at 16 hpi. / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Organ: Lung

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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
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 13.4629 Å
Applied symmetry - Helical parameters - Δ&Phi: -45.1259 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 34.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 3498
ExtractionNumber tomograms: 13 / Number images used: 3498
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING ONLY
Final 3D classificationSoftware - Name: RELION (ver. 5.0 beta3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0 beta3)

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