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- EMDB-63766: Structure of HN HA at pH 7.0 (conformation1). -

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Basic information

Entry
Database: EMDB / ID: EMD-63766
TitleStructure of HN HA at pH 7.0 (conformation1).
Map data
Sample
  • Complex: HN/18 HA
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsinfluenza / HA / cryo-EM / 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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsSun HL / Peng Q / Deng GJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32192452 China
CitationJournal: To Be Published
Title: Structure of HN HA at pH 7.0 (conformation1).
Authors: Sun HL / Peng Q / Deng GJ
History
DepositionMar 15, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63766.png

Downloads & links

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Map

FileDownload / File: emd_63766.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.)
0.82 Å/pix.
x 320 pix.
= 262.4 Å		0.82 Å/pix.
x 320 pix.
= 262.4 Å		0.82 Å/pix.
x 320 pix.
= 262.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.0016695529 - 2.1106973
Average (Standard dev.)0.0014645099 (±0.02860454)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 262.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63766_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_63766_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 : HN/18 HA

EntireName: HN/18 HA
Components
  • Complex: HN/18 HA
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HN/18 HA

SupramoleculeName: HN/18 HA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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: 36.42893 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DTICVGYHAN NSTDTVDTIL EKNVTVTHSV NLLEDSHNGK LCSLNGKIPL QLGNCNVAGW ILGNPKCDLL LTANSWSYII ETSNSKNGA CYPGEFADYE ELKEQLSTVS SFERFEIFPK ATSWPNHDTT RGTTVSCSHS GANSFYRNLL WIVKKGNSYP K LSKSYTNN ...String:
DTICVGYHAN NSTDTVDTIL EKNVTVTHSV NLLEDSHNGK LCSLNGKIPL QLGNCNVAGW ILGNPKCDLL LTANSWSYII ETSNSKNGA CYPGEFADYE ELKEQLSTVS SFERFEIFPK ATSWPNHDTT RGTTVSCSHS GANSFYRNLL WIVKKGNSYP K LSKSYTNN KGKEVLVIWG VHHPPTDSDQ QTLYQNNNTY VSVGSTKYYK RFTPEIVARP KVREQAGRMN YYWTLLDQGD TI TFEATGN LIAPWHAFAL KKGSSSGIMR SDAQVHNCTT KCQTPHGALK GNLPFQNVHP VTIGKCPKYV KSTQLRLATG LRN IPSIQS R

UniProtKB: Hemagglutinin

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Macromolecule #2: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 25.067293 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GLFGAIAGFI EGGWTGMVDG WYGYHHRNEQ GSGYAADQKS TQIAIDGISN KVNSVIEKMN IQFTSVGKEF NSLEKRMENL NKKVDDGFL DVWTYNAELL ILLENERTLD FHDLNVKNLY EKVKSQLRNN AKEIGNGCFE FYHKCDNECM ESVKNGTYNY P KYSEESKL ...String:
GLFGAIAGFI EGGWTGMVDG WYGYHHRNEQ GSGYAADQKS TQIAIDGISN KVNSVIEKMN IQFTSVGKEF NSLEKRMENL NKKVDDGFL DVWTYNAELL ILLENERTLD FHDLNVKNLY EKVKSQLRNN AKEIGNGCFE FYHKCDNECM ESVKNGTYNY P KYSEESKL NREEIDGVKL ESMGIHQILA IYSTVASSLV LLVSLGAISF WMCSNGSLQC RVCI

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: 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: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 BASE (4k 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: 1.5 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: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 227972
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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