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- EMDB-37567: Structure of hemagglutinin from Asiatic toad influenza-like virus... -

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Basic information

Entry
Database: EMDB / ID: EMD-37567
TitleStructure of hemagglutinin from Asiatic toad influenza-like virus complexed with human receptor analog LSTc
Map data
Sample
  • Complex: Toad Hemagglutinin
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHemagglutinin / VIRAL PROTEIN
Function / homologyHaemagglutinin, influenzavirus B / Haemagglutinin / Haemagglutinin, influenzavirus A/B / host cell surface receptor binding / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / membrane / Hemagglutinin
Function and homology information
Biological speciesWuhan asiatic toad influenza virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsZhang D / Xie YF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of hemagglutinin from Asiatic toad influenza-like virus
Authors: Zhang D / Xie YF
History
DepositionSep 25, 2023-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37567.png

Downloads & links

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Map

FileDownload / File: emd_37567.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: 0.65
Minimum - Maximum-4.833528 - 5.9356756
Average (Standard dev.)0.00032207073 (±0.14382426)
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_37567_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_37567_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 : Toad Hemagglutinin

EntireName: Toad Hemagglutinin
Components
  • Complex: Toad Hemagglutinin
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Toad Hemagglutinin

SupramoleculeName: Toad Hemagglutinin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Wuhan asiatic toad influenza virus

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Wuhan asiatic toad influenza virus
Molecular weightTheoretical: 54.95159 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: NQICIGKAIK PINGTVETVS RMAKVTGMKK VGGERMQKIC AKGEQIHDSS SACGIVSHHL KQEGCDFPFL LNKPKFATTG PMNTSTTGF NFYLTEKAKS WMNITWRVLG ENKDFGDNLV EKYGESGATS EGATLKNYYW YVPTAKPGPV VYEKLAECTG T IYYGALLS ...String:
NQICIGKAIK PINGTVETVS RMAKVTGMKK VGGERMQKIC AKGEQIHDSS SACGIVSHHL KQEGCDFPFL LNKPKFATTG PMNTSTTGF NFYLTEKAKS WMNITWRVLG ENKDFGDNLV EKYGESGATS EGATLKNYYW YVPTAKPGPV VYEKLAECTG T IYYGALLS DAEAGYIAVT GRNVTERWDV RFTGSSESSI SFSGPKQSPM EEYIIKSVRS SVDTVRNIII LDSGRVKKGE TF SISLSSG AVVIPTIFCD GDFAVTPQVQ IDKDCASDCH SAYGSFPNGS SFIIHHSVHT VGSCPPSILR NFDVIDGYEA TWE ETKQSR GFFGAILGFF TGGIQGAIDG WYGVTNHDTG KGTAADQTST QKAVEAITNK LNEAIENGNQ RYNQLYGLAR TQAE LLGNL GKEVNDLRLE TFTEFIRLET ILVNTRIIEE HQAIGSKKKE EVKRLLGPNA LDLGNGCFNL THTCDSNCVN SISRG TYTR ENYIHNVTLA GTPKIDGVV

UniProtKB: Hemagglutinin

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / 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
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: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 206720
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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