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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
Function / homology
Function and homology information


Transport of HA trimer, NA tetramer and M2 tetramer from the endoplasmic reticulum to the Golgi Apparatus / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral mRNA Translation ...Transport of HA trimer, NA tetramer and M2 tetramer from the endoplasmic reticulum to the Golgi Apparatus / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral mRNA Translation / viral budding from plasma membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / extracellular region / plasma membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
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: Zheyuan Zhang / Cheng Peng / Weiping Zhang / Jiaming Liang / Kexin Liu / Yong Chen / Junxia Zhang / Rui Liang / Yutong Song / Sai Li /
Abstract: Cryo-ET combined with subtomogram averaging (STA) enables the structural elucidation of macromolecular assemblies in native environments. However, their widespread adoption has been limited by the ...Cryo-ET combined with subtomogram averaging (STA) enables the structural elucidation of macromolecular assemblies in native environments. However, their widespread adoption has been limited by the labor-intensive, expertise-dependent data processing workflow. Here we present FlyTomo, a software that streamlines data processing from frame alignment to STA with high-throughput for authentic cryo-ET scenarios. During data acquisition, FlyTomo performs real-time diagnosis, enabling prompt feedback on sample quality, microscope performance and structural features. After acquisition, it aggregates diagnostic metrics into an overview, guiding users through data review and refinement. FlyTomo also curates raw and processed data into directories to simplify data management and archiving. We validate FlyTomo across a diverse set of authentic cryo-ET samples, including purified enveloped viruses and cryo-lamellae, on multiple microscopes and cameras, achieving structures at resolutions of 3.4 to 7.3 Å. Collectively, by integrating accuracy, scalability and usability, FlyTomo reduces the technical barrier for in situ structural biology using cryo-ET.
History
DepositionOct 15, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 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

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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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Histogram

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Half map: #2

Fileemd_66624_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_66624_half_map_2.map
Projections & Slices
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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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