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- EMDB-41422: CryoEM structure of H7 hemagglutinin from A/Shanghai2/2013 H7N9 i... -

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Basic information

Entry
Database: EMDB / ID: EMD-41422
TitleCryoEM structure of H7 hemagglutinin from A/Shanghai2/2013 H7N9 in complex with a human neutralizing antibody H7.HK1
Map data
Sample
  • Complex: H7 hemagglutinin from A/Shanghai2/2013 H7N9 in complex with a human neutralizing antibody H7.HK1
    • Protein or peptide: H7.HK1 Neutralizing Antibody Heavy Chain
    • Protein or peptide: H7.HK1 Neutralizing Antibody Heavy Chain
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsvirus / antibody / influenza / 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 / 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
Biological speciesHomo sapiens (human) / Influenza A virus (A/Shanghai/02/2013(H7N9))
Methodsingle particle reconstruction / cryo EM / Resolution: 3.62 Å
AuthorsMorano NC / Wu X / Shapiro L
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationPG010737 United States
CitationJournal: Nat Commun / Year: 2024
Title: Human neutralizing antibodies target a conserved lateral patch on H7N9 hemagglutinin head.
Authors: Manxue Jia / Hanjun Zhao / Nicholas C Morano / Hong Lu / Yin-Ming Lui / Haijuan Du / Jordan E Becker / Kwok-Yung Yuen / David D Ho / Peter D Kwong / Lawrence Shapiro / Kelvin Kai-Wang To / Xueling Wu /
Abstract: Avian influenza A virus H7N9 causes severe human infections with >30% fatality. Currently, there is no H7N9-specific prevention or treatment for humans. Here, from a 2013 H7N9 convalescent case in ...Avian influenza A virus H7N9 causes severe human infections with >30% fatality. Currently, there is no H7N9-specific prevention or treatment for humans. Here, from a 2013 H7N9 convalescent case in Hong Kong, we isolate four hemagglutinin (HA)-reactive monoclonal antibodies (mAbs), with three directed to the globular head domain (HA1) and one to the stalk domain (HA2). Two clonally related HA1-directed mAbs, H7.HK1 and H7.HK2, potently neutralize H7N9 and protect female mice from lethal H7N9/AH1 challenge. Cryo-EM structures reveal that H7.HK1 and H7.HK2 bind to a β14-centered surface and disrupt the 220-loop that makes hydrophobic contacts with sialic acid on an adjacent protomer, thereby blocking viral entry. Sequence analysis indicates the lateral patch targeted by H7.HK1 and H7.HK2 to be conserved among influenza subtypes. Both H7.HK1 and H7.HK2 retain HA1 binding and neutralization capacity to later H7N9 isolates from 2016-2017, consistent with structural data showing that the antigenic mutations during this timeframe occur at their epitope peripheries. The HA2-directed mAb H7.HK4 lacks neutralizing activity but when used in combination with H7.HK2 moderately augments female mouse protection. Overall, our data reveal antibodies to a conserved lateral HA1 supersite that confer neutralization, and when combined with a HA2-directed non-neutralizing mAb, augment protection.
History
DepositionAug 2, 2023-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41422.png

Downloads & links

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Map

FileDownload / File: emd_41422.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.128
Minimum - Maximum-0.8192845 - 0.96449476
Average (Standard dev.)0.00068480504 (±0.020224549)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_41422_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41422_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : H7 hemagglutinin from A/Shanghai2/2013 H7N9 in complex with a hum...

EntireName: H7 hemagglutinin from A/Shanghai2/2013 H7N9 in complex with a human neutralizing antibody H7.HK1
Components
  • Complex: H7 hemagglutinin from A/Shanghai2/2013 H7N9 in complex with a human neutralizing antibody H7.HK1
    • Protein or peptide: H7.HK1 Neutralizing Antibody Heavy Chain
    • Protein or peptide: H7.HK1 Neutralizing Antibody Heavy Chain
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: H7 hemagglutinin from A/Shanghai2/2013 H7N9 in complex with a hum...

SupramoleculeName: H7 hemagglutinin from A/Shanghai2/2013 H7N9 in complex with a human neutralizing antibody H7.HK1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: H7.HK1 Neutralizing Antibody Heavy Chain

MacromoleculeName: H7.HK1 Neutralizing Antibody Heavy Chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.856218 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVKPSETLSL TCSVSGGSIN SYYWTWIRQP PGKGLEWVGY IYHSGSTSYN PSLKSRITIS VAPSKNHFSL ELTSMTAAD TAVYYCARLG GHGDYGSDYW GQGTLVTVSS

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Macromolecule #2: H7.HK1 Neutralizing Antibody Heavy Chain

MacromoleculeName: H7.HK1 Neutralizing Antibody Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.153719 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVMTQSPVS LPVTPGEPAS ISCNSSQSLL HSNGYAHLDW YLQKPGQSPK LMIYLGLNRA FGVPDRFSGS GSGTDFTLKI SRVEAEDVG VYYCMQALQT PFTFGPGTRV DIK

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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/Shanghai/02/2013(H7N9))
Molecular weightTheoretical: 63.075688 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNTQILVFAL IAIIPTNADK ICLGHHAVSN GTKVNTLCER GVEVVNATET VERTNIPRIC SKGKRTVDLG QCGLLGTITG PPQCDQFLE FSADLIIERR EGSDVCYPGK FVNEEALRQI LRESGGIDKE AMGFTYSGIR TNGATSSCRR SGSSFYAEMK W LLSNTDNA ...String:
MNTQILVFAL IAIIPTNADK ICLGHHAVSN GTKVNTLCER GVEVVNATET VERTNIPRIC SKGKRTVDLG QCGLLGTITG PPQCDQFLE FSADLIIERR EGSDVCYPGK FVNEEALRQI LRESGGIDKE AMGFTYSGIR TNGATSSCRR SGSSFYAEMK W LLSNTDNA AFPQMTKSYK NTRKNPALIV WGIHHSGSTA EQTKLYGSGN KLVTVGSSNY QQSFVPSPGA RTQVNGQSGR ID FHWLMLN PNDTVTFSFN GAFIAPDRAS FLRGKSMGIQ SGVQVDADCE GDCYYSGGTI ISNLPFQNID SRAVGKCPRY VKQ RSLLLA TGMKNVPEIP KGRRRRRRGL FGAIAGFIEN GWEGLIDGWY GFRHQNAQGE GTAADYKSTQ SAIDCITGKL NRLI EKTNQ QFELIDNEFT EVEKQIGNVI NWTRDSITEV WSYNAELLVA MENQHTIDLA DSEMDKLYER VKRQLRENAE EDGTG CFEI FHKCDDDCMA SIRNNTYDHS KYREEAMQNR IQIDGVSGRL VPRGSPGSGY IPEAPRDGQA YVRKDGEWVL LSTFLG HHH HHH

UniProtKB: Hemagglutinin

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 7 / 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
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.06 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: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6idd

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 178347
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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