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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: Nat Commun / Year: 2025
Title: Visualizing influenza A virus assembly by in situ cryo-electron tomography.
Authors: Moritz Wachsmuth-Melm / Sarah Peterl / Aidan O'Riain / Jana Makroczyová / Konstantin Fischer / Tim Krischuns / Sílvia Vale-Costa / Maria João Amorim / Petr Chlanda /
Abstract: Influenza A virus (IAV) forms pleomorphic particles that package eight ribonucleoprotein complexes (vRNPs), each carrying a distinct RNA genome segment. vRNPs assemble in the nucleus and undergo ...Influenza A virus (IAV) forms pleomorphic particles that package eight ribonucleoprotein complexes (vRNPs), each carrying a distinct RNA genome segment. vRNPs assemble in the nucleus and undergo selective sorting during Rab11a-mediated trafficking to the plasma membrane. Virion assembly is orchestrated by matrix protein 1 (M1), which forms a layer beneath the viral envelope containing hemagglutinin (HA) and neuraminidase (NA). However, molecular details of vRNP distribution, cytosolic trafficking, and coordination of IAV assembly remains unclear. Using in situ cryo-ET, we reveal that HA-containing membranes provide Rab11a-dependent platforms for membrane-assisted vRNP clustering, reducing inter-vRNP distances. In the absence of HA, vRNPs cluster on NA-containing membranes and virus assembly remains intact, indicating that vRNP clustering and trafficking is membrane-assisted but HA independent. The characteristic 7 + 1 vRNP bundle forms concomitantly with budding and is orchestrated by M1 layer assembly that precedes plasma membrane attachment. We further reveal that intracellular M1 forms multilayered helical assemblies of antiparallel dimers, structurally distinct from the M1 layer in virions. These assemblies are compact in the nucleus but partially dissociate in the cytoplasm, likely serving as a reservoir for budding. Together, our findings uncover membrane-assisted vRNP clustering and molecular details of M1 coordinated influenza virus assembly.
History
DepositionOct 8, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing 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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