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- EMDB-65055: Cryo EM structure of hemagglutinin from Puerto Rico/8/1934 (H1N1)... -

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Basic information

Entry
Database: EMDB / ID: EMD-65055
TitleCryo EM structure of hemagglutinin from Puerto Rico/8/1934 (H1N1) in complex with a single domain antibody
Map data
Sample
  • Complex: Binary complex of hemagglutitin from Puerto Rico/8/1934 (H1N1) in complex with a single domain antibody
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: nanobody
KeywordsHemagglutinin / complex / single domain antibody / VIRAL PROTEIN
Function / homology
Function and homology information


Transport of HA trimer, NA tetramer and M2 tetramer from the endoplasmic reticulum to the Golgi Apparatus / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral mRNA Translation ...Transport of HA trimer, NA tetramer and M2 tetramer from the endoplasmic reticulum to the Golgi Apparatus / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral mRNA Translation / viral budding from plasma membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / extracellular region / plasma 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 / Influenza A virus (strain A/Puerto Rico/8/1934 H1N1) / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsYang ZL / Ying TL / Wu YL / Huang KK
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82322001, 82495204 China
CitationJournal: To Be Published
Title: Inhalable and broadly neutralizing single-domain antibodies targeting influenza A hemagglutinin
Authors: Huang KK / Lv MW / Kong Y / Wang MK / Ma XJ / Xu QY / Zhu XY / Li WX / Ying TL / Yang ZL / Wu YL
History
DepositionJun 16, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65055.png

Downloads & links

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Map

FileDownload / File: emd_65055.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 300 pix.
= 279. Å		0.93 Å/pix.
x 300 pix.
= 279. Å		0.93 Å/pix.
x 300 pix.
= 279. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.4504349 - 1.0455481
Average (Standard dev.)0.0014004782 (±0.029288303)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 279.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65055_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_65055_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 : Binary complex of hemagglutitin from Puerto Rico/8/1934 (H1N1) in...

EntireName: Binary complex of hemagglutitin from Puerto Rico/8/1934 (H1N1) in complex with a single domain antibody
Components
  • Complex: Binary complex of hemagglutitin from Puerto Rico/8/1934 (H1N1) in complex with a single domain antibody
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: nanobody

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Supramolecule #1: Binary complex of hemagglutitin from Puerto Rico/8/1934 (H1N1) in...

SupramoleculeName: Binary complex of hemagglutitin from Puerto Rico/8/1934 (H1N1) in complex with a single domain antibody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 240 KDa

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Macromolecule #1: Hemagglutinin HA1 chain

MacromoleculeName: Hemagglutinin HA1 chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)
Molecular weightTheoretical: 36.164734 KDa
Recombinant expressionOrganism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
SequenceString: DTICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCRLKGIAPL QLGKCNIAGW LLGNPECDPL LPVRSWSYIV ETPNSENGI CYPGDFIDYE ELREQLSSVS SFERFEIFPK ESSWPNHNTN GVTAACSHEG KSSFYRNLLW LTEKEGSYPK L KNSYVNKK ...String:
DTICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCRLKGIAPL QLGKCNIAGW LLGNPECDPL LPVRSWSYIV ETPNSENGI CYPGDFIDYE ELREQLSSVS SFERFEIFPK ESSWPNHNTN GVTAACSHEG KSSFYRNLLW LTEKEGSYPK L KNSYVNKK GKEVLVLWGI HHPPNSKEQQ NLYQNENAYV SVVTSNYNRR FTPEIAERPK VRDQAGRMNY YWTLLKPGDT II FEANGNL IAPMYAFALS RGFGSGIITS NASMHECNTK CQTPLGAINS SLPYQNIHPV TIGECPKYVR SAKLRMVTGL RNI PS

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 (strain A/Puerto Rico/8/1934 H1N1)
Molecular weightTheoretical: 20.124369 KDa
Recombinant expressionOrganism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
SequenceString:
IQSRGLFGAI AGFIEGGWTG MIDGWYGYHH QNEQGSGYAA DQKSTQNAIN GITNKVNTVI EKMNIQFTAV GKEFNKLEKR MENLNKKVD DGFLDIWTYN AELLVLLENE RTLDFHDSNV KNLYEKVKSQ LKNNAKEIGN GCFEFYHKCD NECMESVRNG T YDYPKYSE ESKLNRE

UniProtKB: Hemagglutinin

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Macromolecule #3: nanobody

MacromoleculeName: nanobody / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 13.083656 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVKLEESGGG LVQPGGSLRL SCVASGFSFP FAAMNWHRQV PGKERELVAS ISATGDRINY ADSVKGRFTI SRDNLKNTLY LQMSALKPE DSAVYYCNFP RGLEFLDDFW GQGTQVTVSS

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (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: 1.6 µm / Nominal defocus min: 0.8 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 354972
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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