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- EMDB-45555: CryoEM structure of HA trimer from EMPIAR10097, processed with sp... -

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Basic information

Entry
Database: EMDB / ID: EMD-45555
TitleCryoEM structure of HA trimer from EMPIAR10097, processed with spIsoNet
Map data
Sample
  • Complex: Influenza hemagglutinin trimer
Keywordshemagglutinin trimer / MEMBRANE PROTEIN
Biological speciesInfluenza A virus (A/Hong Kong/1/1968(H3N2))
Methodsingle particle reconstruction / cryo EM / Resolution: 4.14 Å
AuthorsLiu YT / Fan HC / Hu JJ / Zhou ZH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
CitationJournal: Nat Methods / Year: 2025
Title: Overcoming the preferred-orientation problem in cryo-EM with self-supervised deep learning.
Authors: Yun-Tao Liu / Hongcheng Fan / Jason J Hu / Z Hong Zhou /
Abstract: While advances in single-particle cryo-EM have enabled the structural determination of macromolecular complexes at atomic resolution, particle orientation bias (the 'preferred' orientation problem) ...While advances in single-particle cryo-EM have enabled the structural determination of macromolecular complexes at atomic resolution, particle orientation bias (the 'preferred' orientation problem) remains a complication for most specimens. Existing solutions have relied on biochemical and physical strategies applied to the specimen and are often complex and challenging. Here, we develop spIsoNet, an end-to-end self-supervised deep learning-based software to address map anisotropy and particle misalignment caused by the preferred-orientation problem. Using preferred-orientation views to recover molecular information in under-sampled views, spIsoNet improves both angular isotropy and particle alignment accuracy during 3D reconstruction. We demonstrate spIsoNet's ability to generate near-isotropic reconstructions from representative biological systems with limited views, including ribosomes, β-galactosidases and a previously intractable hemagglutinin trimer dataset. spIsoNet can also be generalized to improve map isotropy and particle alignment of preferentially oriented molecules in subtomogram averaging. Therefore, without additional specimen-preparation procedures, spIsoNet provides a general computational solution to the preferred-orientation problem.
History
DepositionJun 27, 2024-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45555.png

Downloads & links

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Map

FileDownload / File: emd_45555.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 256 pix.
= 335.36 Å		1.31 Å/pix.
x 256 pix.
= 335.36 Å		1.31 Å/pix.
x 256 pix.
= 335.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.32662347 - 0.41506043
Average (Standard dev.)0.0000019337563 (±0.0060010185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 335.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45555_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Additional map: spIsoNet corrected half map 1

Fileemd_45555_additional_1.map
AnnotationspIsoNet corrected half map 1
Projections & Slices
AxesZYX

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Additional map: spIsoNet corrected half map 2

Fileemd_45555_additional_2.map
AnnotationspIsoNet corrected half map 2
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AxesZYX

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Half map: #1

Fileemd_45555_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45555_half_map_2.map
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Sample components

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Entire : Influenza hemagglutinin trimer

EntireName: Influenza hemagglutinin trimer
Components
  • Complex: Influenza hemagglutinin trimer

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Supramolecule #1: Influenza hemagglutinin trimer

SupramoleculeName: Influenza hemagglutinin trimer / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Influenza A virus (A/Hong Kong/1/1968(H3N2))

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 82.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

8731

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 130000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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