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- EMDB-71579: Subtomogram average of influenza hemagglutinin (A/Puerto Rico/8/1934) -

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Basic information

Entry
Database: EMDB / ID: EMD-71579
TitleSubtomogram average of influenza hemagglutinin (A/Puerto Rico/8/1934)
Map data
Sample
  • Virus: Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Keywordsinfluenza / hemagglutinin / VIRAL PROTEIN
Biological speciesInfluenza A virus (A/Puerto Rico/8/1934(H1N1))
Methodsubtomogram averaging / cryo EM / Resolution: 5.8 Å
AuthorsHuang QJ / Schiffer CA
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM143773 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM151996 United States
CitationJournal: J Vis Exp / Year: 2025
Title: Subnanometer-resolution Structural Determination of Hemagglutinin from Cryo-electron Tomography of Influenza Viruses.
Authors: Qiuyu J Huang / Clint N McDaniel / Alijah A Griffith / Celia A Schiffer / Mohan Somasundaran /
Abstract: Cryo-electron tomography is a powerful tool to visualize heterogeneous samples, with one major application being structural characterization of pleomorphic viruses. In recent years, subtomogram ...Cryo-electron tomography is a powerful tool to visualize heterogeneous samples, with one major application being structural characterization of pleomorphic viruses. In recent years, subtomogram averaging of viral glycoproteins has emerged as a method to directly visualize these crucial proteins on the surface of intact virions. One important target is the hemagglutinin (HA) glycoprotein of influenza virus, which densely covers the viral envelope and is responsible for influenza receptor binding and membrane fusion. While subtomogram averages of influenza HA have been reported, their resolutions have been limited due to the low signal-to-noise ratio inherent to cryoET as well as the manual effort required to analyze heterogenous influenza virions. Presented here is a cryoET analysis pipeline that integrates several software packages to analyze tomographic data of influenza virions efficiently and robustly. This protocol describes the structural determination of HA from influenza virions, through steps from initial motion correction to final model building. Following this pipeline, a HA reconstruction at 6.0 Å resolution was obtained from two cryoET datasets collected from the A/Puerto Rico/8/34 (PR8) influenza strain.
History
DepositionJul 2, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71579.png

Downloads & links

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Map

FileDownload / File: emd_71579.map.gz / Format: CCP4 / Size: 13.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesX (Sec.)Y (Row.)Z (Col.)
2.09 Å/pix.
x 154 pix.
= 321.398 Å		2.09 Å/pix.
x 154 pix.
= 321.398 Å		2.09 Å/pix.
x 154 pix.
= 321.398 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.75
Minimum - Maximum-23.375156 - 24.755030000000001
Average (Standard dev.)0.000000000006763 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions154154154
Spacing154154154
CellA=B=C: 321.39798 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_71579_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71579_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

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Sample components

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Entire : Influenza A virus (A/Puerto Rico/8/1934(H1N1))

EntireName: Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Components
  • Virus: Influenza A virus (A/Puerto Rico/8/1934(H1N1))

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Supramolecule #1: Influenza A virus (A/Puerto Rico/8/1934(H1N1))

SupramoleculeName: Influenza A virus (A/Puerto Rico/8/1934(H1N1)) / type: virus / ID: 1 / Parent: 0
Details: Virus produced in embryonated eggs and purified from allantoic fluid.
NCBI-ID: 211044
Sci species name: Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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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: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE-PROPANE / Instrument: EMS-002 RAPID IMMERSION FREEZER

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.86 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: 6.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 42000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: M / Number subtomograms used: 15970
ExtractionNumber tomograms: 26 / Number images used: 15970 / Software - Name: Warp
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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