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- EMDB-45998: Endo H-treated hemagglutinin A/Hong Kong/1/68 -

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Basic information

Entry
Database: EMDB / ID: EMD-45998
TitleEndo H-treated hemagglutinin A/Hong Kong/1/68
Map datasharpen map of endoH-treated hemagglutinin A/Hong Kong/1/68
Sample
  • Complex: hemagglutinin A/Hong Kong/1/68 trimer
    • Protein or peptide: Hemagglutinin HA1 chain
  • Protein or peptide: Hemagglutinin HA2 chain,Green fluorescent protein fusion
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordshemagglutinin / glycoprotein / H3 / VIRAL PROTEIN
Function / homology
Function and homology information


bioluminescence / viral budding from plasma membrane / generation of precursor metabolites and energy / 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 ...bioluminescence / viral budding from plasma membrane / generation of precursor metabolites and energy / 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 / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Green fluorescent protein / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus / Influenza A virus (strain A/Hong Kong/1/1968 H3N2) / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsTorrents de la Pena A / de Paiva Froes Rocha R / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: To Be Published
Title: Structural and immunological characterization of the H3 influenza hemagglutinin during antigenic drift
Authors: de Paiva Froes Rocha R / Torrents de la Pena A / Ward AB / de Vries RP / Berndsen ZT / Chakraborty S
History
DepositionJul 31, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45998.png

Downloads & links

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Map

FileDownload / File: emd_45998.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpen map of endoH-treated hemagglutinin A/Hong Kong/1/68
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 320 pix.
= 368. Å		1.15 Å/pix.
x 320 pix.
= 368. Å		1.15 Å/pix.
x 320 pix.
= 368. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.0064833 - 3.5798652
Average (Standard dev.)0.000209523 (±0.06458167)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 368.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45998_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: sharpen map of endoH-treated hemagglutinin A/Hong Kong/1/68

Fileemd_45998_half_map_1.map
Annotationsharpen map of endoH-treated hemagglutinin A/Hong Kong/1/68
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: sharpen map of endoH-treated hemagglutinin A/Hong Kong/1/68

Fileemd_45998_half_map_2.map
Annotationsharpen map of endoH-treated hemagglutinin A/Hong Kong/1/68
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : hemagglutinin A/Hong Kong/1/68 trimer

EntireName: hemagglutinin A/Hong Kong/1/68 trimer
Components
  • Complex: hemagglutinin A/Hong Kong/1/68 trimer
    • Protein or peptide: Hemagglutinin HA1 chain
  • Protein or peptide: Hemagglutinin HA2 chain,Green fluorescent protein fusion
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: hemagglutinin A/Hong Kong/1/68 trimer

SupramoleculeName: hemagglutinin A/Hong Kong/1/68 trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Influenza A virus / Strain: A/Hong Kong/1/1968 H3N2

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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/Hong Kong/1/1968 H3N2)
Strain: A/Hong Kong/1/1968 H3N2
Molecular weightTheoretical: 38.523496 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLAQDLPGN DNSTATLCLG HHAVPNGTLV KTITDDQIEV TNATELVQSS STGKICNNPH RILDGIDCT LIDALLGDPH CDVFQNETWD LFVERSKAFS NCYPYDVPDY ASLRSLVASS GTLEFITEGF TWTGVTQNGG S NACKRGPG ...String:
MPMGSLQPLA TLYLLGMLVA SVLAQDLPGN DNSTATLCLG HHAVPNGTLV KTITDDQIEV TNATELVQSS STGKICNNPH RILDGIDCT LIDALLGDPH CDVFQNETWD LFVERSKAFS NCYPYDVPDY ASLRSLVASS GTLEFITEGF TWTGVTQNGG S NACKRGPG SGFFSRLNWL TKSGSTYPVL NVTMPNNDNF DKLYIWGVHH PSTNQEQTSL YVQASGRVTV STRRSQQTII PN IGSRPWV RGLSSRISIY WTIVKPGDVL VINSNGNLIA PRGYFKMRTG KSSIMRSDAP IDTCISECIT PNGSIPNDKP FQN VNKITY GACPKYVKQN TLKLATGMRN VPEKQT

UniProtKB: Hemagglutinin

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Macromolecule #2: Hemagglutinin HA2 chain,Green fluorescent protein fusion

MacromoleculeName: Hemagglutinin HA2 chain,Green fluorescent protein fusion
type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 55.973602 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RGLFGAIAGF IENGWEGMID GWYGFRHQNS EGTGQAADLK STQAAIDQIN GKLNRVIEKT NEKFHQIEKE FSEVEGRIQD LEKYVEDTK IDLWSYNAEL LVALENQHTI DLTDSEMNKL FEKTGRQLRE NAEDMGNGCF KIYHKCDNAC IESIRNGTYD H DVYRDEAL ...String:
RGLFGAIAGF IENGWEGMID GWYGFRHQNS EGTGQAADLK STQAAIDQIN GKLNRVIEKT NEKFHQIEKE FSEVEGRIQD LEKYVEDTK IDLWSYNAEL LVALENQHTI DLTDSEMNKL FEKTGRQLRE NAEDMGNGCF KIYHKCDNAC IESIRNGTYD H DVYRDEAL NNRFQIKGVE LKLELIKRMK QIEDKIEEIE SKQKKIENEI ARIKKIKLVP RGSVDENLYF QAMSKGEELF TG VVPILVE LDGDVNGHKF SVRGEGEGDA TNGKLTLKFI CTTGKLPVPW PTLVTTLTYG VQCFSRYPDH MKRHDFFKSA MPE GYVQER TISFKDDGTY KTRAEVKFEG DTLVNRIELK GIDFKEDGNI LGHKLEYNFN SHNVYITADK QKNGIKANFK IRHN VEDGS VQLADHYQQN TPIGDGPVLL PDNHYLSTQS VLSKDPNEKR DHMVLLEFVT AAGITHGMSS AWSHPQFEKG GGSGG GSGG SAWSHPQFEK

UniProtKB: Hemagglutinin, Green fluorescent protein

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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

Concentration1 mg/mL
BufferpH: 7.4 / Details: TBS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4zcj

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 332294
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4zcj


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9cxu:
Endo H-treated hemagglutinin A/Hong Kong/1/68

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