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- EMDB-47108: H1 influenza HA spike on a nanobicelle -

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Basic information

Entry
Database: EMDB / ID: EMD-47108
TitleH1 influenza HA spike on a nanobicelle
Map dataLocal refinement of HA that is embedded in a nanobicelle.
Sample
  • Complex: Hemagglutinin
KeywordsHemagglutinin / Nanobicelle / Influenza / Vaccine / VIRAL PROTEIN
Biological speciesInfluenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsDearborn AD / Khorrami ND / Gallagher JR / Harris AK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)ZIAAI001370-01 United States
CitationJournal: To Be Published
Title: Structure-guided assembly of an influenza spike nanobicelle vaccine provides pan H1 intranasal protection
Authors: Myers ML / Gallagher JR / Woolfork DD / Khorrami ND / Park WB / Maldonado-Puga S / Bohrnsen E / Schwarz BH / Alves DA / Bock KW / Dearborn AD / Harris AK
History
DepositionSep 23, 2024-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47108.png

Downloads & links

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Map

FileDownload / File: emd_47108.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal refinement of HA that is embedded in a nanobicelle.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 320 pix.
= 422.4 Å		1.32 Å/pix.
x 320 pix.
= 422.4 Å		1.32 Å/pix.
x 320 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.85726637 - 1.3691778
Average (Standard dev.)0.0019886817 (±0.026104594)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47108_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B from a local refinement of...

Fileemd_47108_half_map_1.map
AnnotationHalf map B from a local refinement of HA that is embedded in a nanobicelle.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A from a local refinement of...

Fileemd_47108_half_map_2.map
AnnotationHalf map A from a local refinement of HA that is embedded in a nanobicelle.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hemagglutinin

EntireName: Hemagglutinin
Components
  • Complex: Hemagglutinin

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Supramolecule #1: Hemagglutinin

SupramoleculeName: Hemagglutinin / type: complex / ID: 1 / Parent: 0
Details: Trimer of Influenza A virus H1 Hemagglutinin embedded in a nanobicelle
Source (natural)Organism: Influenza A virus / Strain: H1 / Organ: egg
Molecular weightTheoretical: 240 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

Concentration0.9 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
8.0 g/LNaClsodium chloride
0.2 g/LKClpotassium chloride
1.44 g/LNa2HPO4disodium phosphate
0.245 g/LKH2PO4monopotassium phosphate

Details: 137mM NaCl, 2.7mM KCl, 10mM Na2HPO4, 1.8mM KH2PO4
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 40 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278.15 K / Instrument: LEICA EM GP
DetailsThis sample was localized about the periphery of each nanobicelle and contextually distinct from free HA trimers.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number real images: 5217 / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2464958
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 51 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 294312
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final 3D classificationNumber classes: 100 / Avg.num./class: 42706 / Software - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

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