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- EMDB-49155: Deconvolution of an Influenza hemagglutinin (HA) trimer reconstru... -

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Basic information

Entry
Database: EMDB / ID: EMD-49155
TitleDeconvolution of an Influenza hemagglutinin (HA) trimer reconstruction (emd-8731)
Map dataemd_8731 map processed with deconvolution and sharpening
Sample
  • Complex: influenza hemagglutinin (HA) trimer
KeywordsDeconvolution / Anisotropic resolution / VIRAL PROTEIN
Biological speciesInfluenza A virus (A/Hong Kong/1/1968(H3N2))
Methodsingle particle reconstruction / cryo EM / Resolution: 4.25 Å
AuthorsCheng Y / Li J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM140847 United States
CitationJournal: bioRxiv / Year: 2025
Title: Deconvolution to restore cryo-EM maps with anisotropic resolution.
Authors: Junrui Li / Yifei Chen / Shawn Zheng / Angus McDonald / John W Sedat / David A Agard / Yifan Cheng /
Abstract: With technological advancements in recent years, single particle cryogenic electron microscopy (cryo-EM) has become a major methodology for structural biology. Structure determination by single ...With technological advancements in recent years, single particle cryogenic electron microscopy (cryo-EM) has become a major methodology for structural biology. Structure determination by single particle cryo-EM is premised on randomly orientated particles embedded in thin layer of vitreous ice to resolve high-resolution structural information in all directions. Otherwise, preferentially distributed particle orientations will lead to anisotropic resolution of the structure. Here we established a deconvolution approach, named AR-Decon, to computationally improve the quality of three-dimensional maps with anisotropic resolutions reconstructed from datasets with preferred orientations. We have tested and validated the procedure with both synthetic and experimental datasets and compared its performance with alternative machine-learning based methods.
History
DepositionFeb 10, 2025-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49155.png

Downloads & links

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Map

FileDownload / File: emd_49155.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationemd_8731 map processed with deconvolution and sharpening
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (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)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 12.9
Minimum - Maximum-18.189789999999999 - 53.977499999999999
Average (Standard dev.)-0.000000000002154 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Additional map: emd 8731 map processed with deconvolution

Fileemd_49155_additional_1.map
Annotationemd_8731 map processed with deconvolution
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: emd 8731 map processed with deconvolution, sharpening and EMReady

Fileemd_49155_additional_2.map
Annotationemd_8731 map processed with deconvolution, sharpening and EMReady
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Original emd 8731 primary map

Fileemd_49155_additional_3.map
AnnotationOriginal emd_8731 primary map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Original emd 8731 half-map for dFSC calculation

Fileemd_49155_half_map_1.map
AnnotationOriginal emd_8731 half-map for dFSC calculation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Original emd 8731 half-map for dFSC calculation

Fileemd_49155_half_map_2.map
AnnotationOriginal emd_8731 half-map for dFSC calculation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : influenza hemagglutinin (HA) trimer

EntireName: influenza hemagglutinin (HA) trimer
Components
  • Complex: influenza hemagglutinin (HA) trimer

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Supramolecule #1: influenza hemagglutinin (HA) trimer

SupramoleculeName: influenza hemagglutinin (HA) trimer / type: complex / ID: 1 / Parent: 0
Details: This is not an experimental map, but a map obtained by applying deconvolution to the original experimental map EMD-8731
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

MicroscopeTFS 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

8731

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.25 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 287820
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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