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- EMDB-46500: Map of hemagglutinin A/Sing/INFIMH/16 expressed in 293F cells -

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Basic information

Entry
Database: EMDB / ID: EMD-46500
TitleMap of hemagglutinin A/Sing/INFIMH/16 expressed in 293F cells
Map datamap of influenza hemagglutinin A/Sing/INFIMH/16 expressed in 293F
Sample
  • Complex: trimer of influenza hemagglutinin A/Sing/INFIMH/16
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsinfluenza / hemagglutinin / evolution / VIRAL PROTEIN
Function / homology
Function and homology information


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 / 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: 3.8 Å
AuthorsTorrents de la Pena A / Ward AB / de Paiva Froes Rocha R
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
History
DepositionAug 8, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46500.png

Downloads & links

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Map

FileDownload / File: emd_46500.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap of influenza hemagglutinin A/Sing/INFIMH/16 expressed in 293F
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 540 pix.
= 564.3 Å		1.05 Å/pix.
x 540 pix.
= 564.3 Å		1.05 Å/pix.
x 540 pix.
= 564.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0035
Minimum - Maximum-0.004456039 - 0.0153386425
Average (Standard dev.)0.0000036393697 (±0.00028167947)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 564.3 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46500_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map of influenza hemagglutinin A/Sing/INFIMH/16 expressed in...

Fileemd_46500_half_map_1.map
Annotationhalf map of influenza hemagglutinin A/Sing/INFIMH/16 expressed in 293F
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map of influenza hemagglutinin A/Sing/INFIMH/16 expressed in...

Fileemd_46500_half_map_2.map
Annotationhalf map of influenza hemagglutinin A/Sing/INFIMH/16 expressed in 293F
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : trimer of influenza hemagglutinin A/Sing/INFIMH/16

EntireName: trimer of influenza hemagglutinin A/Sing/INFIMH/16
Components
  • Complex: trimer of influenza hemagglutinin A/Sing/INFIMH/16
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: trimer of influenza hemagglutinin A/Sing/INFIMH/16

SupramoleculeName: trimer of influenza hemagglutinin A/Sing/INFIMH/16 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: C3
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: 92.743625 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLAATLCLG HHAVPNGTIV KTITNDRIEV TNATELVQNS SIGEICDSPH QILDGENCTL IDALLGDPQ CDGFQNKKWD LFVERSKAYS NCYPYDVPDY ASLRSLVASS GTLEFKNESF NWTGVTQNGT SSACIRGSSS S FFSRLNWL ...String:
MPMGSLQPLA TLYLLGMLVA SVLAATLCLG HHAVPNGTIV KTITNDRIEV TNATELVQNS SIGEICDSPH QILDGENCTL IDALLGDPQ CDGFQNKKWD LFVERSKAYS NCYPYDVPDY ASLRSLVASS GTLEFKNESF NWTGVTQNGT SSACIRGSSS S FFSRLNWL THLNYTYPAL NVTMPNKEQF DKLYIWGVHH PGTDKDQIFL YAQSSGRITV STKRSQQAVI PNIGSRPRIR DI PSRISIY WTIVKPGDIL LINSTGNLIA PRGYFKIRSG KSSIMRSDAP IGKCKSECIT PNGSIPNDKP FQNVNRITYG ACP RYVKHS TLKLATGMRN VPEKQTRGIF GAIAGFIENG WEGMVDGWYG FRHQNSEGRG QAADLKSTQA AIDQINGKLN RLIG KTNEK FHQIEKEFSE VEGRVQDLEK YVEDTKIDLW SYNAELLVAL ENQHTIDLTD SEMNKLFEKT KKQLRENAED MGNGC FKIY HKCDNACIES IRNETYDHNV YRDEALNNRF QIKRMKQIED KIEEIESKQK KIENEIARIK KIKLVPRGSV DENLYF QAM SKGEELFTGV VPILVELDGD VNGHKFSVRG EGEGDATNGK LTLKFICTTG KLPVPWPTLV TTLTYGVQCF SRYPDHM KR HDFFKSAMPE GYVQERTISF KDDGTYKTRA EVKFEGDTLV NRIELKGIDF KEDGNILGHK LEYNFNSHNV YITADKQK N GIKANFKIRH NVEDGSVQLA DHYQQNTPIG DGPVLLPDNH YLSTQSVLSK DPNEKRDHMV LLEFVTAAGI THGMSSAWS HPQFEKGGGS GGGSGGSAWS HPQFEK

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: 21 / 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

Concentration7 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 TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1313732
CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4m4y

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 76978
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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