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- EMDB-33024: Cryo-EM structure of H1 hemagglutinin from A/Washington/05/2011 i... -

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Basic information

Entry
Database: EMDB / ID: EMD-33024
TitleCryo-EM structure of H1 hemagglutinin from A/Washington/05/2011 in complex with a neutralizing antibody 28-12
Map data
Sample
  • Complex: H1 hemagglutinin from A/Washington/05/2011 in complex with a neutralizing antibody 28-12
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Heavy chain of antibody 12 fab
    • Protein or peptide: The light chain of antibody 12 fab
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCong Y / Liu CX
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29040300 China
CitationJournal: Nat Commun / Year: 2022
Title: Unique binding pattern for a lineage of human antibodies with broad reactivity against influenza A virus.
Authors: Xiaoyu Sun / Caixuan Liu / Xiao Lu / Zhiyang Ling / Chunyan Yi / Zhen Zhang / Zi Li / Mingliang Jin / Wenshuai Wang / Shubing Tang / Fangfang Wang / Fang Wang / Sonam Wangmo / Shuangfeng ...Authors: Xiaoyu Sun / Caixuan Liu / Xiao Lu / Zhiyang Ling / Chunyan Yi / Zhen Zhang / Zi Li / Mingliang Jin / Wenshuai Wang / Shubing Tang / Fangfang Wang / Fang Wang / Sonam Wangmo / Shuangfeng Chen / Li Li / Liyan Ma / Yaguang Zhang / Zhuo Yang / Xiaoping Dong / Zhikang Qian / Jianping Ding / Dayan Wang / Yao Cong / Bing Sun /
Abstract: Most structurally characterized broadly neutralizing antibodies (bnAbs) against influenza A viruses (IAVs) target the conserved conformational epitopes of hemagglutinin (HA). Here, we report a ...Most structurally characterized broadly neutralizing antibodies (bnAbs) against influenza A viruses (IAVs) target the conserved conformational epitopes of hemagglutinin (HA). Here, we report a lineage of naturally occurring human antibodies sharing the same germline gene, V3-48/V1-12. These antibodies broadly neutralize the major circulating strains of IAV in vitro and in vivo mainly by binding a contiguous epitope of H3N2 HA, but a conformational epitope of H1N1 HA, respectively. Our structural and functional studies of antibody 28-12 revealed that the continuous amino acids in helix A, particularly N49 of H3 HA, are critical to determine the binding feature with 28-12. In contrast, the conformational epitope feature is dependent on the discontinuous segments involving helix A, the fusion peptide, and several HA1 residues within H1N1 HA. We report that this antibody was initially selected by H3 (group 2) viruses and evolved via somatic hypermutation to enhance the reactivity to H3 and acquire cross-neutralization to H1 (group 1) virus. These findings enrich our understanding of different antigenic determinants of heterosubtypic influenza viruses for the recognition of bnAbs and provide a reference for the design of influenza vaccines and more effective antiviral drugs.
History
DepositionMar 7, 2022-
Header (metadata) releaseMar 23, 2022-
Map releaseMar 23, 2022-
UpdateJun 22, 2022-
Current statusJun 22, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33024.png

Downloads & links

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Map

FileDownload / File: emd_33024.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.318 Å
Density
Contour LevelBy AUTHOR: 0.00749
Minimum - Maximum-0.0017475953 - 2.1778939
Average (Standard dev.)0.0019503103 (±0.031814214)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 289.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : H1 hemagglutinin from A/Washington/05/2011 in complex with a neut...

EntireName: H1 hemagglutinin from A/Washington/05/2011 in complex with a neutralizing antibody 28-12
Components
  • Complex: H1 hemagglutinin from A/Washington/05/2011 in complex with a neutralizing antibody 28-12
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Heavy chain of antibody 12 fab
    • Protein or peptide: The light chain of antibody 12 fab

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Supramolecule #1: H1 hemagglutinin from A/Washington/05/2011 in complex with a neut...

SupramoleculeName: H1 hemagglutinin from A/Washington/05/2011 in complex with a neutralizing antibody 28-12
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Influenza A virus
Recombinant expressionOrganism: Insecta environmental sample (insect)

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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: 37.055742 KDa
Recombinant expressionOrganism: Insecta environmental sample (insect)
SequenceString: TFATANSDTL CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDKHNGKLCK LRGVAPLHLG KCNIAGWILG NPECESLSTA SSWSYIVET SSSDNGTCYP GDFIDYEELR EQLSSVSSFE RFEIFPKTSS WPNHDSNKGV TAACPHAGAK GFYKNLIWLV K KGNSYPKL ...String:
TFATANSDTL CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDKHNGKLCK LRGVAPLHLG KCNIAGWILG NPECESLSTA SSWSYIVET SSSDNGTCYP GDFIDYEELR EQLSSVSSFE RFEIFPKTSS WPNHDSNKGV TAACPHAGAK GFYKNLIWLV K KGNSYPKL SKSYINDKGK EVLVLWGIHH PSTTADQQSL YQNADTYVFV GTSRYSKKFK PEIAIRPKVR DQEGRMNYYW TL VEPGDKI TFEATGNLVV PRYAFAMERN AGSGIIISDT PVHDCNTTCQ TPKGAINTSL PFQNIHPITI GKCPKYVKST KLR LATGLR NVPSIQSR

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Macromolecule #2: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus / Strain: A/Freiburg/728006/2011(H1N1)
Molecular weightTheoretical: 20.160332 KDa
Recombinant expressionOrganism: Insecta environmental sample (insect)
SequenceString:
GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADLKS TQNAIDKITN KVNSVIEKMN TQFTAVGKEF NHLEKRIENL NKKVDDGFL DIWTYNAELL VLLENERTLD YHDSNVKNLY EKVRNQLKNN AKEIGNGCFE FYHKCDNTCM ESVKNGTYDY P KYSEEAKL NREEIDGV

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Macromolecule #3: Heavy chain of antibody 12 fab

MacromoleculeName: Heavy chain of antibody 12 fab / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.466277 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EVQLVESGGG LVQPGGSLRL SCAASGFTFS TYNMNWVRQA PGKGLEWLSY ISTSSNTIYY ADSVKGRFTI SRDNAKNSLF LQMNSLRDE DTAVYYCARD RGCSSTNCYV VGYYFYGMDV WGQGTTVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT ...String:
EVQLVESGGG LVQPGGSLRL SCAASGFTFS TYNMNWVRQA PGKGLEWLSY ISTSSNTIYY ADSVKGRFTI SRDNAKNSLF LQMNSLRDE DTAVYYCARD RGCSSTNCYV VGYYFYGMDV WGQGTTVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV E

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Macromolecule #4: The light chain of antibody 12 fab

MacromoleculeName: The light chain of antibody 12 fab / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.264861 KDa
Recombinant expressionOrganism: Insecta environmental sample (insect)
SequenceString: DIQMTQSPSS VSASVGDRVT ITCRASQGIS SYLAWYQLKP GRAPKLLIYG ATRLQSGVPS RFSGSGSGTD FTLTISGLQP EDFATYHCQ QADSFPLTFG QGTRLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSS VSASVGDRVT ITCRASQGIS SYLAWYQLKP GRAPKLLIYG ATRLQSGVPS RFSGSGSGTD FTLTISGLQP EDFATYHCQ QADSFPLTFG QGTRLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 124947
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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