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- EMDB-51553: Structure of uncleaved Influenza A/Victoria/2570/2019 Haemaggluti... -

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Basic information

Entry
Database: EMDB / ID: EMD-51553
TitleStructure of uncleaved Influenza A/Victoria/2570/2019 Haemagglutinin- The 2021 Influenza A(H1N1)pdm09 egg-derived vaccine candidate.
Map datasharpened map used for model building
Sample
  • Virus: Influenza A virus
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsglycoprotein / viral receptor / fusion protein / HA / VIRAL PROTEIN
Function / homology
Function and homology information


viral budding from plasma membrane / 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 / 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 speciesH1N1 subtype (virus) / Influenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsWaraich K / Meir A / Petrov F / Akbar S / Smith T / Anne Scott K / Dibben O / Bhella D
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Other private United Kingdom
CitationJournal: To Be Published
Title: Structure of uncleaved Influenza A/Victoria/2570/2019 Haemagglutinin. The 2021 Influenza A(H1N1)pdm09 egg-derived vaccine candidate.
Authors: Waraich K / Meir A / Petrov F / Akbar S / Smith T / Anne Scott K / Dibben O / Bhella D
History
DepositionSep 16, 2024-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51553.png

Downloads & links

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Map

FileDownload / File: emd_51553.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map used for model building
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 250 pix.
= 253.75 Å		1.02 Å/pix.
x 250 pix.
= 253.75 Å		1.02 Å/pix.
x 250 pix.
= 253.75 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.015 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00859
Minimum - Maximum-0.042636182 - 0.07655323
Average (Standard dev.)0.000029126264 (±0.002172468)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 253.75 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 2 flipped and scaled after calibration of pixel size

Fileemd_51553_half_map_1.map
Annotationhalf map 2 flipped and scaled after calibration of pixel size
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1 flipped and scaled after calibration of pixel size

Fileemd_51553_half_map_2.map
Annotationhalf map 1 flipped and scaled after calibration of pixel size
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 A virus

EntireName: Influenza A virus
Components
  • Virus: Influenza A virus
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Influenza A virus

SupramoleculeName: Influenza A virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 11320 / Sci species name: Influenza A virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Molecular weightTheoretical: 420 kDa/nm

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: H1N1 subtype (virus)
Molecular weightTheoretical: 63.550672 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKAILVVMLY TFTTANADTL CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDKHNGKLCK LRGVAPLHLG KCNIAGWILG NPECESLST ARSWSYIVET SNSDNGTCYP GDFINYEELR EQLSSVSSFE RFEIFPKTSS WPNHDSDNGV TAACPHAGAK S FYKNLIWL ...String:
MKAILVVMLY TFTTANADTL CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDKHNGKLCK LRGVAPLHLG KCNIAGWILG NPECESLST ARSWSYIVET SNSDNGTCYP GDFINYEELR EQLSSVSSFE RFEIFPKTSS WPNHDSDNGV TAACPHAGAK S FYKNLIWL VKKGKSYPKI NQTYINDKGK EVLVLWGIHH PPTIADQQSL YQNADAYVFV GTSRYSKKFK PEIATRPKVR DR EGRMNYY WTLVEPGDKI TFEATGNLVA PRYAFTMERD AGSGIIISDT PVHDCNTTCQ TPEGAINTSL PFQNVHPITI GKC PKYVKS TKLRLATGLR NVPSIQSRGL FGAIAGFIEG GWTGMVDGWY GYHHQNEQGS GYAADLKSTQ NAIDKITNKV NSVI EKMNT QFTAVGKEFN HLEKRIENLN KKVDDGFLDI WTYNAELLVL LENERTLDYH DSNVKNLYEK VRNQLKNNAK EIGNG CFEF YHKCDNTCME SVKNGTYDYP KYSEEAKLNR EKIDGVKLDS TRIYQILAIY STVASSLVLV VSLGAISFWM CSNGSL QCR ICI

UniProtKB: Hemagglutinin

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 8
Details: 0.15 M NaCl, 25 mM Tris-HCl pH 8, and 0.1% beta-octylglucoside (BOG)
GridModel: C-flat-2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 10 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: DIRECT ELECTRON APOLLO (4k x 4k) / Number real images: 3741 / Average electron dose: 68.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number images used: 163054
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: SwissModel / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9gsp:
Structure of uncleaved Influenza A/Victoria/2570/2019 Haemagglutinin. The 2021 Influenza A(H1N1)pdm09 egg-derived vaccine candidate.

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