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- EMDB-35733: H7N9 HA-1H9 Fab -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-35733
TitleH7N9 HA-1H9 Fab
Map dataThe cryoEM structure of HA-1H9 complex
Sample
  • Complex: The complex of H7N9 HA-1H9 Fab
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: 1H9 Fab heavy chain
    • Protein or peptide: 1H9 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 / 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 speciesH7N9 subtype (virus) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsZhao BB / Sun ZZ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32272980 China
CitationJournal: To Be Published
Title: H7N9 HA-1H9 Fab
Authors: Zhao BB / Sun ZZ
History
DepositionMar 25, 2023-
Header (metadata) releaseApr 24, 2024-
Map releaseApr 24, 2024-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35733.png

Downloads & links

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Map

FileDownload / File: emd_35733.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe cryoEM structure of HA-1H9 complex
Voxel sizeX=Y=Z: 1.076 Å
Density
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.87267 - 1.6041479
Average (Standard dev.)-0.00043224232 (±0.024580747)
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 HA-1H9 complex

Fileemd_35733_half_map_1.map
AnnotationThe half A map of HA-1H9 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 HA-1H9 complex

Fileemd_35733_half_map_2.map
AnnotationThe half B map of HA-1H9 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: 1H9 Fab heavy chain
    • Protein or peptide: 1H9 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: 1H9 Fab heavy chain

MacromoleculeName: 1H9 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.339751 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
MVQLQESGPG LVKPSQSLSL TCTVTGYSIT SDYTWNWIRQ FPGNKLEWMG YITYSDTTSY NPSLKSRISI TRDTSKNQFF LQLNSVTTE DTATYYCARS DGWYGFAYWG QGTLVTVSA

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Macromolecule #3: 1H9 Fab light chain

MacromoleculeName: 1H9 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.661016 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
DIQMNQSPSS LSASLGDTIT ITCHASQNIN VWLSWYQQKP GNIPKLLIYK AFDLHTGVPS RFSGSGSGTG FTLTISSLQP EDIATYYCQ QGQTYPFTFG 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 / N-Acetylglucosamine

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 179237

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