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- EMDB-33023: Cryo-EM structure of H3 hemagglutinin from A/HongKong/01/1968 in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-33023
TitleCryo-EM structure of H3 hemagglutinin from A/HongKong/01/1968 in complex with a neutralizing antibody 28-12
Map data
Sample
  • Complex: Cryo-EM structure of H3 hemagglutinin from A/HongKong/01/1968 in complex with a neutralizing antibody 28-12
    • Protein or peptide: Heavy chain of antibody 12 fab
    • Protein or peptide: The light chain of the antibody 12 fab
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Hemagglutinin
KeywordsH3 hemagglutinin / A/HongKong/01/1968 / antibody 28-12 / cryo-EM / STRUCTURAL PROTEIN
Function / homology
Function and homology information


viral budding from plasma membrane / 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 / virion 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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus / Homo sapiens (human) / Influenza A virus (A/Hong Kong/1/1968(H3N2))
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33023.png

Downloads & links

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Map

FileDownload / File: emd_33023.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 220 pix.
= 289.96 Å		1.32 Å/pix.
x 220 pix.
= 289.96 Å		1.32 Å/pix.
x 220 pix.
= 289.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.318 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.0017330695 - 2.0130777
Average (Standard dev.)0.002211234 (±0.033341747)
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 : Cryo-EM structure of H3 hemagglutinin from A/HongKong/01/1968 in ...

EntireName: Cryo-EM structure of H3 hemagglutinin from A/HongKong/01/1968 in complex with a neutralizing antibody 28-12
Components
  • Complex: Cryo-EM structure of H3 hemagglutinin from A/HongKong/01/1968 in complex with a neutralizing antibody 28-12
    • Protein or peptide: Heavy chain of antibody 12 fab
    • Protein or peptide: The light chain of the antibody 12 fab
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Hemagglutinin

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Supramolecule #1: Cryo-EM structure of H3 hemagglutinin from A/HongKong/01/1968 in ...

SupramoleculeName: Cryo-EM structure of H3 hemagglutinin from A/HongKong/01/1968 in complex with a neutralizing antibody 28-12
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Influenza A virus

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Macromolecule #1: Heavy chain of antibody 12 fab

MacromoleculeName: Heavy chain of antibody 12 fab / type: protein_or_peptide / ID: 1 / 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 #2: The light chain of the antibody 12 fab

MacromoleculeName: The light chain of the antibody 12 fab / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.264861 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
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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Macromolecule #3: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Hong Kong/1/1968(H3N2)) / Strain: A/Hong Kong/1/1968 H3N2
Molecular weightTheoretical: 36.218664 KDa
Recombinant expressionOrganism: Insecta environmental sample (insect)
SequenceString: QDLPGNDNPT ATLCLGHHAV PNGTLVKTIT DDQIEVTNAT ELVQSSSTGK ICNNPHRILD GIDCTLIDAL LGDPHCDVFQ NETWDLFVE RSKAFSNCYP YDVPDYASLR SLVASSGTLE FITEGFTWTG VTQNGGSNAC KRGPGSGFFS RLNWLTKSGS T YPVLNVTM ...String:
QDLPGNDNPT ATLCLGHHAV PNGTLVKTIT DDQIEVTNAT ELVQSSSTGK ICNNPHRILD GIDCTLIDAL LGDPHCDVFQ NETWDLFVE RSKAFSNCYP YDVPDYASLR SLVASSGTLE FITEGFTWTG VTQNGGSNAC KRGPGSGFFS RLNWLTKSGS T YPVLNVTM PNNDNFDKLY IWGVHHPSTN QEQTSLYVQA SGRVTVSTRR SQQTIIPNIG SRPWVRGLSS RISIYWTIVK PG DVLVINS NGNLIAPRGY FKMRTGKSSI MRSDAPIDTC ISECITPNGS IPNDKPFQNV NKITYGACPK YVKQNTLKLA TGM RNVPEK QTR

UniProtKB: Hemagglutinin

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Macromolecule #4: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 20.297455 KDa
Recombinant expressionOrganism: Insecta environmental sample (insect)
SequenceString:
GLFGAIAGFI ENGWEGMIDG WYGFRHQNSE GTGQAADLKS TQAAIDQING KLNRVIEKTN EKFHQIEKEF SEVEGRIQDL EKYVEDTKI DLWSYNAELL VALENQHTID LTDSEMNKLF EKTRRQLREN AEDMGNGCFK IYHKCDNACI ESIRNGTYDH D VYRDEALN NRFQIKGV

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

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

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 105383
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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