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- EMDB-46477: Map of influenza hemagglutinin A/Sing/INFIMH/16 expressed in GntI... -

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Basic information

Entry
Database: EMDB / ID: EMD-46477
TitleMap of influenza hemagglutinin A/Sing/INFIMH/16 expressed in GntI- cells
Map datamap of influenza hemagglutinin A/Sing/INFIMH/16 expressed in GntI- cells
Sample
  • Complex: influenza hemagglutinin A/Sing/INFIMH/16 expressed in GntI- cells trimer
    • Protein or peptide: Hemagglutinin
Keywordsinfluenza / H3 / Sing16 / 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: 3.7 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: Torrents de la Pena A / de Paiva Froes Rocha R / Ward AB
History
DepositionAug 7, 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_46477.png

Downloads & links

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Map

FileDownload / File: emd_46477.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap of influenza hemagglutinin A/Sing/INFIMH/16 expressed in GntI- cells
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 360 pix.
= 414. Å		1.15 Å/pix.
x 360 pix.
= 414. Å		1.15 Å/pix.
x 360 pix.
= 414. 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: 0.2
Minimum - Maximum-0.828837 - 1.6759356
Average (Standard dev.)0.00023488127 (±0.024943905)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 414.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46477_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_46477_half_map_1.map
Annotationhalf map of influenza hemagglutinin A/Sing/INFIMH/16 expressed in GntI- cells
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_46477_half_map_2.map
Annotationhalf map of influenza hemagglutinin A/Sing/INFIMH/16 expressed in GntI- cells
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : influenza hemagglutinin A/Sing/INFIMH/16 expressed in GntI- cells...

EntireName: influenza hemagglutinin A/Sing/INFIMH/16 expressed in GntI- cells trimer
Components
  • Complex: influenza hemagglutinin A/Sing/INFIMH/16 expressed in GntI- cells trimer
    • Protein or peptide: Hemagglutinin

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Supramolecule #1: influenza hemagglutinin A/Sing/INFIMH/16 expressed in GntI- cells...

SupramoleculeName: influenza hemagglutinin A/Sing/INFIMH/16 expressed in GntI- cells trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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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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
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 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: 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:

4m4y

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 58645
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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