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- EMDB-66624: Structure of hemagglutinin from influenza A virions determined by... -

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Basic information

Entry
Database: EMDB / ID: EMD-66624
TitleStructure of hemagglutinin from influenza A virions determined by sub-tomogram averaging
Map dataHA map
Sample
  • Complex: Structure of hemagglutinin from influenza A virions determined by sub-tomogram averaging
KeywordsHA / FLU / VIRUS / VIRAL PROTEIN
Biological speciesInfluenza A virus (A/ Puerto Rico/8/34 (H1N1))
Methodsubtomogram averaging / cryo EM / Resolution: 3.6 Å
AuthorsZhang Z / Chen Y
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32241031 China
National Natural Science Foundation of China (NSFC)82241066 China
National Natural Science Foundation of China (NSFC)32171195 China
CitationJournal: Nat Commun / Year: 2026
Title: FlyTomo: a streamlined software for on-the-fly cryo-ET data processing and diagnosis
Authors: Zhang Z / Peng C / Zhang W / Liang J / Liu K / Chen Y / Zhang J / Liang R / Song Y / Li S
History
DepositionOct 15, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66624.png

Downloads & links

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Map

FileDownload / File: emd_66624.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHA map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 237.824 Å		0.93 Å/pix.
x 256 pix.
= 237.824 Å		0.93 Å/pix.
x 256 pix.
= 237.824 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.929 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0375
Minimum - Maximum-0.041636962 - 0.18196708
Average (Standard dev.)0.000000000000071 (±0.008075364)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 237.824 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66624_msk_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_66624_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66624_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of hemagglutinin from influenza A virions determined by...

EntireName: Structure of hemagglutinin from influenza A virions determined by sub-tomogram averaging
Components
  • Complex: Structure of hemagglutinin from influenza A virions determined by sub-tomogram averaging

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Supramolecule #1: Structure of hemagglutinin from influenza A virions determined by...

SupramoleculeName: Structure of hemagglutinin from influenza A virions determined by sub-tomogram averaging
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Influenza A virus (A/ Puerto Rico/8/34 (H1N1))

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 3.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm
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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number subtomograms used: 97201
ExtractionNumber tomograms: 65 / Number images used: 260571 / Software - Name: RELION (ver. 4)
CTF correctionType: PHASE FLIPPING ONLY
Final angle assignmentType: MAXIMUM LIKELIHOOD

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