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- EMDB-35734: H7N9 HA-2D7 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-35734
TitleH7N9 HA-2D7 Fab
Map dataThe cryoEM of H7N9 HA-2D7 Fab complex
Sample
  • Complex: The complex of H7N9 HA-1H9 Fab
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: 2D7 Fab heavy chain
    • Protein or peptide: 2D7 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsH7N9 / HA / Neutralizing antibody / complex / MEMBRANE PROTEIN / MEMBRANE 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 speciesH7N9 subtype (virus) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZhao BB / Sun ZZ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32272980 China
CitationJournal: J Virol / Year: 2025
Title: Structural basis of different neutralization capabilities of monoclonal antibodies against H7N9 virus.
Authors: Bingbing Zhao / Zhenzhao Sun / Shida Wang / Zhibin Shi / Yongping Jiang / Xiurong Wang / Guohua Deng / Peirong Jiao / Hualan Chen / Jingfei Wang /
Abstract: Neutralizing antibodies (nAbs) are important for the treatment of emerging viral diseases and for effective vaccine development. In this study, we generated and evaluated three nAbs (1H9, 2D7, and ...Neutralizing antibodies (nAbs) are important for the treatment of emerging viral diseases and for effective vaccine development. In this study, we generated and evaluated three nAbs (1H9, 2D7, and C4H4) against H7N9 influenza viruses and found that they differ in their ability to inhibit viral attachment, membrane fusion, and egress. We resolved the cryo-electron microscopy (cryo-EM) structures of H7N9 hemagglutinin (HA) alone and in complex with the nAb antigen-binding fragments (Fabs) and identified the HA head-located epitope for each nAb, thereby revealing the molecular basis and key residues that determine the differences in these nAbs in neutralizing H7N9 viruses. Moreover, we found that the humanized nAb CC4H4 provided complete protection in mice against death caused by a lethal H7N9 virus infection, even when nAb was given 3 days after the mice were infected. These findings provide new insights into the neutralizing mechanism and structural basis for the rational design of H7N9 virus vaccines and therapeutics.IMPORTANCEH7N9 viruses have caused severe infections in both birds and humans since their emergence in early 2013 in China. Their persistent presence and variation in avian populations pose a significant threat to both poultry and humans. There are no treatments for human infections. In this study, we thoroughly investigated the neutralization mechanisms, structural basis, and therapeutic effects of three nAbs (1H9, 2D7, and C4H4) against H7N9 viruses. We revealed the molecular determinants underlying the varied performances of the three nAbs in neutralizing H7N9 viruses and protecting H7N9-infected mice. These insights provide a solid foundation for the rational design of vaccines and therapeutics against H7N9 viruses.
History
DepositionMar 25, 2023-
Header (metadata) releaseApr 24, 2024-
Map releaseApr 24, 2024-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35734.png

Downloads & links

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Map

FileDownload / File: emd_35734.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe cryoEM of H7N9 HA-2D7 Fab complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 400 pix.
= 430.4 Å		1.08 Å/pix.
x 400 pix.
= 430.4 Å		1.08 Å/pix.
x 400 pix.
= 430.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.076 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.42572433 - 0.92065024
Average (Standard dev.)-0.00035620044 (±0.013820817)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 430.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: The half A map of H7N9 HA-2D7 Fab complex

Fileemd_35734_half_map_1.map
AnnotationThe half A map of H7N9 HA-2D7 Fab complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The half B map of H7N9 HA-2D7 Fab complex

Fileemd_35734_half_map_2.map
AnnotationThe half B map of H7N9 HA-2D7 Fab complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The complex of H7N9 HA-1H9 Fab

EntireName: The complex of H7N9 HA-1H9 Fab
Components
  • Complex: The complex of H7N9 HA-1H9 Fab
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: 2D7 Fab heavy chain
    • Protein or peptide: 2D7 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: The complex of H7N9 HA-1H9 Fab

SupramoleculeName: The complex of H7N9 HA-1H9 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: H7N9 subtype (virus)

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: H7N9 subtype (virus)
Molecular weightTheoretical: 54.963367 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: DKICLGHHAV SNGTKVNTLT ERGVEVVNAT ETVERTNTPR ICSKGKRTVD LGQCGLLGTI TGPPQCDQFL EFSADLIIER REGSDVCYP GKFVNEEALR QILRESGGID KESMGFTYNG IRTNGVTSAC RRSGSSFYAE MKWLLSNTDN AAFPQMTKSY K NTRESPAI ...String:
DKICLGHHAV SNGTKVNTLT ERGVEVVNAT ETVERTNTPR ICSKGKRTVD LGQCGLLGTI TGPPQCDQFL EFSADLIIER REGSDVCYP GKFVNEEALR QILRESGGID KESMGFTYNG IRTNGVTSAC RRSGSSFYAE MKWLLSNTDN AAFPQMTKSY K NTRESPAI IVWGIHHSVS TAEQTKLYGS GNKLVTVGSS NYQQSFVPSP GARPQVNGLS GRIDFHWLIL NPNDTVTFSF NG AFIAPDR ASFLRGKSMG IQSGVQVDAN CEGDCYHSGG TIISNLPFQN IDSRAVGKCP RYVKQRSLLL ATGMKNVPEV PKG KRTARG LFGAIAGFIE NGWEGLIDGW YGFRHQNAQG EGTAADYKST QSAIDQITGK LNRLIAKTNQ QFKLIDNEFN EVEK QIGNV INWTRDSITE VWSYNAELLV AMENQHTIDL ADSEMDKLYE RVKRQLRENA EEDGTGCFEI FHKCDDDCMA SIRNN TYDH RKYREEAMQN

UniProtKB: Hemagglutinin

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Macromolecule #2: 2D7 Fab heavy chain

MacromoleculeName: 2D7 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.193651 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
MVQLQESGPG LVKPSQSLSL TCTVTGYSIT SDYTWNWIRQ FPGNKLEWMG YISYSGSTSY NPSLKSRMSI TRDTSKNQFL LQLNSVTTA DTATYYCTRD GPYWHIDVWG AGTTVTVSS

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Macromolecule #3: 2D7 Fab light chain

MacromoleculeName: 2D7 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.557938 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
DIQMNQSPSS LSASLGDTIT ITCHASQTIN IWLSWYQLKP GNIPKLLIYK ASNLHTGVPS RFSGSGSGTG FTLTISSLQP EDIASYYCQ QGQSFPYTFG GGTKLEIK

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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: 3 / 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: 8
VitrificationCryogen name: NITROGEN

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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: 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: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 160967
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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