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- EMDB-38311: Dual receptor-binding, infectivity, and transmissibility of an em... -

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Basic information

Entry
Database: EMDB / ID: EMD-38311
TitleDual receptor-binding, infectivity, and transmissibility of an emerging H2N2 avian influenza virus
Map data
Sample
  • Complex: The structure of influenza H2 human Korea hemagglutinin with human receptor
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsH2N2 / influenza virus / receptor / replication / transmission / mice / guinea pig / ferret / mutation / public health risk / VIRUS / 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 speciesInfluenza A virus (strain A/Korea/426/1968 H2N2)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsSun J / Zheng TY
Funding support China, 2 items
OrganizationGrant numberCountry
Chinese Academy of Sciences151C53KYSB20210023 China
Chinese Academy of SciencesYSBR-086 China
CitationJournal: To Be Published
Title: Dual receptor-binding, infectivity, and transmissibility of an emerging H2N2 avian influenza virus
Authors: Sun J
History
DepositionDec 14, 2023-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38311.png

Downloads & links

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Map

FileDownload / File: emd_38311.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.209
Minimum - Maximum-0.0017208369 - 1.7473191
Average (Standard dev.)0.0012985051 (±0.02588861)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38311_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38311_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The structure of influenza H2 human Korea hemagglutinin with huma...

EntireName: The structure of influenza H2 human Korea hemagglutinin with human receptor
Components
  • Complex: The structure of influenza H2 human Korea hemagglutinin with human receptor
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: The structure of influenza H2 human Korea hemagglutinin with huma...

SupramoleculeName: The structure of influenza H2 human Korea hemagglutinin with human receptor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Influenza A virus (strain A/Korea/426/1968 H2N2)

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (strain A/Korea/426/1968 H2N2) / Strain: A/Korea/426/1968 H2N2
Molecular weightTheoretical: 56.322328 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DQICIGYHAN NSTEKIDTIL ERNVTVTHAK DILEKTHNGK LCKLNGIPPL ELGDCSIAGW LLGNPECDRL LRVPEWSYIM EKENPRYSL CYPGSFNDYE ELKHLLSSVK HFEKVKILPK DRWTQHTTTG GSMACAVSGK PSFFRNMVWL TTKGPNYPVA Q GSYNNTSG ...String:
DQICIGYHAN NSTEKIDTIL ERNVTVTHAK DILEKTHNGK LCKLNGIPPL ELGDCSIAGW LLGNPECDRL LRVPEWSYIM EKENPRYSL CYPGSFNDYE ELKHLLSSVK HFEKVKILPK DRWTQHTTTG GSMACAVSGK PSFFRNMVWL TTKGPNYPVA Q GSYNNTSG EQMLIIWGVH HPNDEAEQRA LYQKVGTYVS ASTSTLYKRS IPEIAARPKV NGLGSRMEFS WTLLDMWDTI NF ESTGNLV APEYGFKISK RGSSGIMKTE GTLENCETKC QTPLGAINTT LPFHNVHPLT IGECPKYVKS EKLVLATGLR NVP QIESRG LFGAIAGFIE GGWQGMVDGW YGYHHSNDQG SGYAADKEST QKAFDGITNK VNSVIEKMNT QFEAVGKEFS NLEK RLENL NKKMEDGFLD VWTYNAELLV LMENERTLDF HDSNVKNLYD KVRMQLRDNV KELGNGCFEF YHKCDNECMD SVKNG TYDY PKYEEESKLN RNE

UniProtKB: Hemagglutinin

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 8 / 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

Concentration0.2 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 499159
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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