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- EMDB-33831: Cryo-EM structure of the HA trimer of A/Beijing/262/1995(H1N1) in... -

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Basic information

Entry
Database: EMDB / ID: EMD-33831
TitleCryo-EM structure of the HA trimer of A/Beijing/262/1995(H1N1) in complex with neutralizing antibody 12H5
Map data
Sample
  • Complex: Cryo-EM structure of the HA trimer of A/Beijing/262/1995(H1N1) in complex with neutralizing antibody 12H5
    • Complex: HA trimer of A/Beijing/262/1995(H1N1)
      • Protein or peptide: Hemagglutinin
    • Complex: neutralizing antibody 12H5
      • Protein or peptide: 12H5 light chain
      • Protein or peptide: 12H5 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsInfluenza virus / Hemagglutinin / neutralizing antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / 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
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 (A/Beijing/262/1995(H1N1)) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsZheng Q / Li S / Li T / Xue W / Sun H
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Identification of a cross-neutralizing antibody that targets the receptor binding site of H1N1 and H5N1 influenza viruses.
Authors: Tingting Li / Junyu Chen / Qingbing Zheng / Wenhui Xue / Limin Zhang / Rui Rong / Sibo Zhang / Qian Wang / Minqing Hong / Yuyun Zhang / Lingyan Cui / Maozhou He / Zhen Lu / Zhenyong Zhang / ...Authors: Tingting Li / Junyu Chen / Qingbing Zheng / Wenhui Xue / Limin Zhang / Rui Rong / Sibo Zhang / Qian Wang / Minqing Hong / Yuyun Zhang / Lingyan Cui / Maozhou He / Zhen Lu / Zhenyong Zhang / Xin Chi / Jinjin Li / Yang Huang / Hong Wang / Jixian Tang / Dong Ying / Lizhi Zhou / Yingbin Wang / Hai Yu / Jun Zhang / Ying Gu / Yixin Chen / Shaowei Li / Ningshao Xia /
Abstract: Influenza A viruses pose a significant threat globally each year, underscoring the need for a vaccine- or antiviral-based broad-protection strategy. Here, we describe a chimeric monoclonal antibody, ...Influenza A viruses pose a significant threat globally each year, underscoring the need for a vaccine- or antiviral-based broad-protection strategy. Here, we describe a chimeric monoclonal antibody, C12H5, that offers neutralization against seasonal and pandemic H1N1 viruses, and cross-protection against some H5N1 viruses. Notably, C12H5 mAb offers broad neutralizing activity against H1N1 and H5N1 viruses by controlling virus entry and egress, and offers protection against H1N1 and H5N1 viral challenge in vivo. Through structural analyses, we show that C12H5 engages hemagglutinin (HA), the major surface glycoprotein on influenza, at a distinct epitope overlapping the receptor binding site and covering the 140-loop. We identified eight highly conserved (~90%) residues that are essential for broad H1N1 recognition, with evidence of tolerance for Asp or Glu at position 190; this site is a molecular determinant for human or avian host-specific recognition and this tolerance endows C12H5 with cross-neutralization potential. Our results could benefit the development of antiviral drugs and the design of broad-protection influenza vaccines.
History
DepositionJul 13, 2022-
Header (metadata) releaseAug 17, 2022-
Map releaseAug 17, 2022-
UpdateJul 19, 2023-
Current statusJul 19, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33831.png

Downloads & links

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Map

FileDownload / File: emd_33831.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.78 Å/pix.
x 440 pix.
= 342.32 Å		0.78 Å/pix.
x 440 pix.
= 342.32 Å		0.78 Å/pix.
x 440 pix.
= 342.32 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.778 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.9383156 - 1.3085314
Average (Standard dev.)-0.000056375782 (±0.024705825)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 342.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33831_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33831_half_map_2.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the HA trimer of A/Beijing/262/1995(H1N1) in...

EntireName: Cryo-EM structure of the HA trimer of A/Beijing/262/1995(H1N1) in complex with neutralizing antibody 12H5
Components
  • Complex: Cryo-EM structure of the HA trimer of A/Beijing/262/1995(H1N1) in complex with neutralizing antibody 12H5
    • Complex: HA trimer of A/Beijing/262/1995(H1N1)
      • Protein or peptide: Hemagglutinin
    • Complex: neutralizing antibody 12H5
      • Protein or peptide: 12H5 light chain
      • Protein or peptide: 12H5 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of the HA trimer of A/Beijing/262/1995(H1N1) in...

SupramoleculeName: Cryo-EM structure of the HA trimer of A/Beijing/262/1995(H1N1) in complex with neutralizing antibody 12H5
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: HA trimer of A/Beijing/262/1995(H1N1)

SupramoleculeName: HA trimer of A/Beijing/262/1995(H1N1) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Influenza A virus (A/Beijing/262/1995(H1N1))

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Supramolecule #3: neutralizing antibody 12H5

SupramoleculeName: neutralizing antibody 12H5 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: 12H5 light chain

MacromoleculeName: 12H5 light chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.990588 KDa
SequenceString:
QIQLVQSGPE LKKPGETVRI SCKASGYTFT KNGMNWVQQA PGKGLKWVGW INTYTGEPSY ADDFKGRFAF SLETSASTAY LQINNLKNE DMAAYFCARM VRDAMDFWGQ GTSVTVSS

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Macromolecule #2: 12H5 heavy chain

MacromoleculeName: 12H5 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.249454 KDa
SequenceString:
DIVLTQSPAS LAVSLGQRAT ISCKASQSVD FDGYNYLNWY QQKPGQPPKL LIYAASNLES GIPARFSGSG SGTDFTLNIH PVEEEDAAT YFCQQSNEDP YTFGGGTKLE IKRA

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Macromolecule #3: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Beijing/262/1995(H1N1))
Molecular weightTheoretical: 62.091484 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAAD LGSDTICIGY HANNSTDTVD TVLEKNVTVT HSVNLLEDSH NGKLCLLKG IAPLQLGNCS VAGWILGNPE CESLISKESW SYIVETPNPE NGTCYPGYFA DYEELREQLS SVSSFERFEI F PKESSWPK ...String:
MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAAD LGSDTICIGY HANNSTDTVD TVLEKNVTVT HSVNLLEDSH NGKLCLLKG IAPLQLGNCS VAGWILGNPE CESLISKESW SYIVETPNPE NGTCYPGYFA DYEELREQLS SVSSFERFEI F PKESSWPK HTVTGVTASC SHNGKSSFYR NLLWLTEKNG LYPNLSNSYV NNKEKEVLVL WGVHHPSNIG DQRAIYHTEN AY VSVVSSH YSRRFTPEIA KRPKVRGQEG RINYYWTLLE PGDTIIFEAN GNLIAPWYAF ALSRGFGSGI ITSNAPMNEC DAK CQTPQG AINSSLPFQN VHPVTIGECP KYVRSTKLRM VTGLRNIPSI QSRGLFGAIA GFIEGGWTGM MDGWYGYHHQ NEQG SGYAA DQKSTQNAIN GITNKVNSVI EKMNTQFTAV GKEFNKLERR MENLNKKVDD GFLDIWTYNA ELLVLLENER TLDFH DSNV KNLYEKVKSQ LKNNAKEIGN GCFEFYHKCN NECMESVKNG TYDYPKYSEE SKLNREKIDS GRLVPRGSPG S

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: 4 / 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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 137484
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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