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- EMDB-44894: Influenza hemagglutinin B/Maryland/2016 glycoprotein -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-44894
TitleInfluenza hemagglutinin B/Maryland/2016 glycoprotein
Map datamap of influenza hemagglutinin B/Maryland/2016 glycoprotein
Sample
  • Complex: influenza hemagglutinin B/Maryland/2016 glycoprotein
    • Protein or peptide: Hemagglutinin HA1
  • Protein or peptide: Hemagglutinin HA2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordshemagglutinin / influenza / complex / VIRAL PROTEIN
Function / homology
Function and homology information


host cell surface receptor binding / endocytosis involved in viral entry into host cell / 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 B / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesInfluenza B virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsTorrents de la Pena A / Sewall LM / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI136621C3 United States
Bill & Melinda Gates FoundationINV-002916 United States
CitationJournal: Nat Biomed Eng / Year: 2025
Title: Rapid and High-Throughput Imaging of Immune Complexes Using Microfluidics and Single Particle Electron Microscopy
Authors: Sewall LM / Torrents de la Pena A / Ward AB
History
DepositionMay 15, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44894.png

Downloads & links

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Map

FileDownload / File: emd_44894.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap of influenza hemagglutinin B/Maryland/2016 glycoprotein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 512 pix.
= 367.616 Å		0.72 Å/pix.
x 512 pix.
= 367.616 Å		0.72 Å/pix.
x 512 pix.
= 367.616 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.718 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.20126183 - 0.46851784
Average (Standard dev.)-0.00024513734 (±0.008368521)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 367.616 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44894_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: sharpen map for influenza hemagglutinin B/Maryland/2016 glycoprotein

Fileemd_44894_additional_1.map
Annotationsharpen map for influenza hemagglutinin B/Maryland/2016 glycoprotein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map of influenza hemagglutinin B/Maryland/2016 glycoprotein

Fileemd_44894_half_map_1.map
Annotationhalf map of influenza hemagglutinin B/Maryland/2016 glycoprotein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map of influenza hemagglutinin B/Maryland/2016 glycoprotein

Fileemd_44894_half_map_2.map
Annotationhalf map of influenza hemagglutinin B/Maryland/2016 glycoprotein
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 B/Maryland/2016 glycoprotein

EntireName: influenza hemagglutinin B/Maryland/2016 glycoprotein
Components
  • Complex: influenza hemagglutinin B/Maryland/2016 glycoprotein
    • Protein or peptide: Hemagglutinin HA1
  • Protein or peptide: Hemagglutinin HA2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: influenza hemagglutinin B/Maryland/2016 glycoprotein

SupramoleculeName: influenza hemagglutinin B/Maryland/2016 glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: HA1 and HA2 are two subunits of the same protomer
Source (natural)Organism: Influenza B virus

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Macromolecule #1: Hemagglutinin HA1

MacromoleculeName: Hemagglutinin HA1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza B virus / Strain: B/Maryland/2016
Molecular weightTheoretical: 39.957883 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLADRICTG ITSSNSPHVV KTATQGEVNV TGVIPLTTTP TKSHFANLKG TETRGKLCPK CLNCTDLDV ALGRPKCTGK IPSARVSILH EVRPVTSGCF PIMHDRTKIR QLPNLLRGYE HVRLSTHNVI NAEDAPGGPY K IGTSGSCP ...String:
MPMGSLQPLA TLYLLGMLVA SVLADRICTG ITSSNSPHVV KTATQGEVNV TGVIPLTTTP TKSHFANLKG TETRGKLCPK CLNCTDLDV ALGRPKCTGK IPSARVSILH EVRPVTSGCF PIMHDRTKIR QLPNLLRGYE HVRLSTHNVI NAEDAPGGPY K IGTSGSCP NITNGNGFFA TMAWAVPDNK KTATNPLTIE VPYVCTEGED QITVWGFHSD NETQMAKLYG DSKPQKFTSS AN GVTTHYV SQIGGFPNQT EDGGLPQSGR IVVDYMVQKS GKTGTITYQR GILLPQKVWC ASGRSKVIKG SLPLIGEADC LHE KYGGLN KSKPYYTGEH AKAIGNCPIW VKTPLKLANG TKYRPPAKLL KERG

UniProtKB: Hemagglutinin

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Macromolecule #2: Hemagglutinin HA2

MacromoleculeName: Hemagglutinin HA2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza B virus / Strain: B/Maryland/2016
Molecular weightTheoretical: 24.825535 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FFGAIAGFLE GGWEGMIAGW HGYTSHGAHG VAVAADLKST QEAINKITKN LNSLSELEVK NLQRLSGAMD ELHNEILELD EKVDDLRAD TISSQIELAV LLSNEGIINS EDEHLLALER KLKKMLGPSA VEIGNGCFET KHKCNQTCLD RIAAGTFDAG E FSLPTFDS ...String:
FFGAIAGFLE GGWEGMIAGW HGYTSHGAHG VAVAADLKST QEAINKITKN LNSLSELEVK NLQRLSGAMD ELHNEILELD EKVDDLRAD TISSQIELAV LLSNEGIINS EDEHLLALER KLKKMLGPSA VEIGNGCFET KHKCNQTCLD RIAAGTFDAG E FSLPTFDS LNITAASLND DGLDENLYFQ GSSFLVQSGD GRHHHHHHHH WSHPQFEKWS HPQFEK

UniProtKB: Hemagglutinin

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 6 / 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

Concentration0.02 mg/mL
BufferpH: 7.4 / Details: TBS
GridModel: EMS Lacey Carbon / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: wait time 30 sec, double blot for 4.5s, blot force 1.

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 815 / 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 / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 190000

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 16096
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9bto:
Influenza hemagglutinin B/Maryland/2016 glycoprotein

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