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- EMDB-65056: Cryo EM structure of hemagglutinin from Puerto Rico/8/1934-New Yo... -

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Basic information

Entry
Database: EMDB / ID: EMD-65056
TitleCryo EM structure of hemagglutinin from Puerto Rico/8/1934-New York/55/2004 (H3N2) in complex with a single domain antibody
Map data
Sample
  • Complex: Binary complex of hemagglutinin from Puerto Rico/8/1934-New York/55/2004 (H3N2) in complex with a single domain antibody
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: nanobody
KeywordsHemagglutinin / Complex / Single domain antibody / 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 / Influenza A virus (A/New York/55/2004(H3N2)) / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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_65056.png

Downloads & links

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Map

FileDownload / File: emd_65056.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: 0.12
Minimum - Maximum-0.5472109 - 1.2852825
Average (Standard dev.)-0.0013695564 (±0.035781186)
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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Additional map: local refinement

Fileemd_65056_additional_1.map
Annotationlocal refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65056_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_65056_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 hemagglutinin from Puerto Rico/8/1934-New York/...

EntireName: Binary complex of hemagglutinin from Puerto Rico/8/1934-New York/55/2004 (H3N2) in complex with a single domain antibody
Components
  • Complex: Binary complex of hemagglutinin from Puerto Rico/8/1934-New York/55/2004 (H3N2) in complex with a single domain antibody
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: nanobody

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Supramolecule #1: Binary complex of hemagglutinin from Puerto Rico/8/1934-New York/...

SupramoleculeName: Binary complex of hemagglutinin from Puerto Rico/8/1934-New York/55/2004 (H3N2) 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

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/New York/55/2004(H3N2))
Molecular weightTheoretical: 35.741266 KDa
Recombinant expressionOrganism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
SequenceString: NSTATLCLGH HAVPNGTIVK TITNDQIEVT NATELVQSSS TGGICDSPHQ ILDGENCTLI DALLGDPQCD GFQNKKWDLF VERSKAYSN CYPYDVPDYA SLRSLVASSG TLEFNNESFN WTGVTQNGTS SSCKRRSNNS FFSRLNWLTH LKFKYPALNV T MPNNEKFD ...String:
NSTATLCLGH HAVPNGTIVK TITNDQIEVT NATELVQSSS TGGICDSPHQ ILDGENCTLI DALLGDPQCD GFQNKKWDLF VERSKAYSN CYPYDVPDYA SLRSLVASSG TLEFNNESFN WTGVTQNGTS SSCKRRSNNS FFSRLNWLTH LKFKYPALNV T MPNNEKFD KLYIWGVHHP VTDNDQIRLY AQASGRITVS TKRSQQTVIP NIGSRPRVRD IPSRISIYWT IVKPGDILLI NS TGNLIAP RGYFKIRSGK SSIMRSDAPI GKCNSECITP NGSIPNDKPF QNVNRITYGA CPRYVKQNTL KLATGMRNVP EKQ T

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 (A/New York/55/2004(H3N2))
Molecular weightTheoretical: 19.766928 KDa
Recombinant expressionOrganism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
SequenceString:
RGIFGAIAGF IENGWEGMVD GWYGFRHQNS EGIGQAADLK STQAAINQIN GKLNRLIGKT NEKFHQIEKE FSEVEGRIQD LEKYVEDTK IDLWSYNAEL LVALENQHTI DLTDSEMNKL FERTKKQLRE NAEDMGNGCF KIYHKCDNAC IGSIRNGTYD H DVYRDEAL NNRF

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: 12.481842 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EVQLVESGGD SVQPGGSLRL SCAASGSIFH INGMGWYRQA PGRQRELVAA IFSGGSTNYA DSVKGRFTIS GDNAKNTAYL QMNSLKPED TAVYYCAARK WTGNVWAFWG QGTQVTV

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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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 385561
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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