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- EMDB-38008: Cryo-EM structure of H5 hemagglutinin from human-infecting H5N8 i... -

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Basic information

Entry
Database: EMDB / ID: EMD-38008
TitleCryo-EM structure of H5 hemagglutinin from human-infecting H5N8 influenza virus in complex with Sialyl-Lewis X
Map data
Sample
  • Complex: H5 hemagglutinin from human-infecting H5N8 influenza virus in complex with Sialyl-Lewis X
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsVIRAL PROTEIN-IMMUNE SYSTEM COMPLEX
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
Methodsingle particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsJin XY / Han P / Song H / Qi JX
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82122040 China
CitationJournal: To Be Published
Title: Enhanced binding of Sialyl Lewis X to hemagglutinin contributes to H5N8 mammalian pathogenicity and infectivity
Authors: Jin X / Han P / Zhang C / Maio AD / Shi Y / Qi J / Bi Y / Liu Y / Song H / Gao GF
History
DepositionNov 9, 2023-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38008.png

Downloads & links

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Map

FileDownload / File: emd_38008.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 384 pix.
= 264.96 Å		0.69 Å/pix.
x 384 pix.
= 264.96 Å		0.69 Å/pix.
x 384 pix.
= 264.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.69 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.2643958 - 0.82245463
Average (Standard dev.)-0.001721998 (±0.027779177)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 264.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38008_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38008_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 : H5 hemagglutinin from human-infecting H5N8 influenza virus in com...

EntireName: H5 hemagglutinin from human-infecting H5N8 influenza virus in complex with Sialyl-Lewis X
Components
  • Complex: H5 hemagglutinin from human-infecting H5N8 influenza virus in complex with Sialyl-Lewis X
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: H5 hemagglutinin from human-infecting H5N8 influenza virus in com...

SupramoleculeName: H5 hemagglutinin from human-infecting H5N8 influenza virus in complex with Sialyl-Lewis X
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Influenza A 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: Influenza A virus
Molecular weightTheoretical: 57.687926 KDa
Recombinant expressionOrganism: Baculovirus transfer vector pFASTBAC1
SequenceString: DQICIGYHAN NSTEQVDTIM EKNVTVTHAQ DILEKTHNGK LCDLNGVKPL ILKDCSVAGW LLGNPMCDEF IRVPEWSYIV ERANPANDL CYPGSLNDYE ELKHLLSRIN HFEKILIIPK SSWPNHETSL GVSAACPYQG APSFFRNVVW LIKKNDAYPT I KISYNNTN ...String:
DQICIGYHAN NSTEQVDTIM EKNVTVTHAQ DILEKTHNGK LCDLNGVKPL ILKDCSVAGW LLGNPMCDEF IRVPEWSYIV ERANPANDL CYPGSLNDYE ELKHLLSRIN HFEKILIIPK SSWPNHETSL GVSAACPYQG APSFFRNVVW LIKKNDAYPT I KISYNNTN REDLLILWGI HHSNNAEEQT NLYKNPTTYI SVGTSTLNQR LVPKIATRSQ VNGQRGRMDF FWTILKPDDA IH FESNGNF IAPEYAYKIV KKGDSTIMKS GVEYGHCNTK CQTPVGAINS SMPFHNIHPL TIGECPKYVK SNKLVLATGL RNS PLREKR RKRGLFGAIA GFIEGGWQGM VDGWYGYHHS NEQGSGYAAD KESTQKAIDG VTNKVNSIID KMNTQFEAVG REFN NLERR IENLNKKMED GFLDVWTYNA ELLVLMENER TLDFHDSNVK NLYDKVRLQL RDNAKELGNG CFEFYHKCDN ECMES VRNG TYDYPQYSEE ARLKREEISG VK

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: 7 / 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 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 362087
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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