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- EMDB-54831: Cryo-EM map of influenza hemagglutinin (A/Hong Kong/1/1968, H3N2)... -

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Basic information

Entry
Database: EMDB / ID: EMD-54831
TitleCryo-EM map of influenza hemagglutinin (A/Hong Kong/1/1968, H3N2) following ultrasonic excitation
Map dataSharpened consensus map
Sample
  • Complex: Recombinant influenza hemagglutinin
Keywordsinfluenza hemagglutinin / preferred orientation / ultrasonic excitation / VIRAL PROTEIN
Biological speciesInfluenza A virus (A/Hong Kong/01/1968(H3N2))
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsWilliams HM / Curtis WA / Haubner M / Hruby J / Drabbels M / Lorenz UJ
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationTMCG-2_213773 Switzerland
CitationJournal: bioRxiv / Year: 2025
Title: Overcoming Preferred Orientation in Cryo-EM With Ultrasonic Excitation During Vitrification.
Authors: Harry M Williams / Wyatt A Curtis / Michal Haubner / Jakub Hruby / Marcel Drabbels / Ulrich J Lorenz /
Abstract: Preferred particle orientation remains a frequently encountered issue in cryo-electron microscopy that arises when proteins adsorb to the air-water interface in only a limited number of orientations. ...Preferred particle orientation remains a frequently encountered issue in cryo-electron microscopy that arises when proteins adsorb to the air-water interface in only a limited number of orientations. This can significantly increase the data acquisition time required to reach a desired resolution or even make it impossible to obtain a reconstruction altogether. Here, we show that preferred orientation can be overcome by continuously exciting the sample with ultrasonic waves during vitrification. Our experiments suggest that mechanical oscillations induced in the sample support continuously shake proteins loose form the air-water interface, thereby scrambling their orientations. The simple, physical nature of this mechanism should make it applicable to a wide range of proteins. Since our method can be easily implemented in existing vitrification devices, it should find widespread adoption.
History
DepositionAug 20, 2025-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54831.png

Downloads & links

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Map

FileDownload / File: emd_54831.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened consensus map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.97566164 - 1.4973661
Average (Standard dev.)-0.0003915637 (±0.033825487)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54831_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_54831_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_54831_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Recombinant influenza hemagglutinin

EntireName: Recombinant influenza hemagglutinin
Components
  • Complex: Recombinant influenza hemagglutinin

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Supramolecule #1: Recombinant influenza hemagglutinin

SupramoleculeName: Recombinant influenza hemagglutinin / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Influenza A virus (A/Hong Kong/01/1968(H3N2))
Molecular weightTheoretical: 225 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
137.0 mMNaClSodium chloride
2.7 mMKClPotassium chloride
10.0 mMNa2HPO4Sodium phosphate dibasic
1.8 mMKH2PO4Potassium phosphate monobasic

Details: 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, and 1.8 mM KH2PO4, pH 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K
Details: The sample was vitrified using our in-house Vitrobot Mark IV modified through the addition of a jetting assembly..

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 96000
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

Particle selectionNumber selected: 2847316
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 28251
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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