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- EMDB-39762: Structure of human 18_14D scFv and 1G01 scFv in complex with infl... -

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Basic information

Entry
Database: EMDB / ID: EMD-39762
TitleStructure of human 18_14D scFv and 1G01 scFv in complex with influenza virus neuraminidase from A/Yunan/DQ001/2016 (H5N6)
Map data
Sample
  • Complex: Structure of human 18_14D C and 1G01 scFv in complex with influenza virus neuraminidase from A/Yunan/DQ001/2016 (H5N6)
    • Protein or peptide: Neuraminidase
    • Protein or peptide: Light chain of 18_14D scFv
    • Protein or peptide: Heavy chain of 18_14D scFv
    • Protein or peptide: Heavy chain of 1G01 scFv
    • Protein or peptide: Light chain of 1G01 scFv
  • Ligand: CALCIUM ION
Keywordsinfluenza virus / neuraminidase / human monoclonal antibody / immunogen / VIRAL PROTEIN
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesInfluenza A virus (A/Yunan/DQ001/2016 (H5N6)) / Influenza A virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsWang M / Peng Q / Gao Y / Shi Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32192452 China
CitationJournal: Nat Commun / Year: 2024
Title: A human monoclonal antibody targeting the monomeric N6 neuraminidase confers protection against avian H5N6 influenza virus infection.
Authors: Min Wang / Yuan Gao / Chenguang Shen / Wei Yang / Qi Peng / Jinlong Cheng / Han-Ming Shen / Yang Yang / George Fu Gao / Yi Shi /
Abstract: The influenza neuraminidase (NA) is a potential target for the development of a next-generation influenza vaccine, but its antigenicity is not well understood. Here, we isolate an anti-N6 human ...The influenza neuraminidase (NA) is a potential target for the development of a next-generation influenza vaccine, but its antigenicity is not well understood. Here, we isolate an anti-N6 human monoclonal antibody, named 18_14D, from an H5N6 avian influenza virus (AIV) infected patient. The antibody weakly inhibits enzymatic activity but confers protection in female mice, mainly via ADCC function. The cryo-EM structure shows that 18_14D binds to a unique epitope on the lateral surface of the N6 tetramer, preventing the formation of tightly closed NA tetramers. These findings contribute to the molecular understanding of protective immune responses to NA of AIVs in humans and open an avenue for the rational design of NA-based vaccines.
History
DepositionApr 17, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39762.png

Downloads & links

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Map

FileDownload / File: emd_39762.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 262.4 Å		0.82 Å/pix.
x 320 pix.
= 262.4 Å		0.82 Å/pix.
x 320 pix.
= 262.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.0017897475 - 2.5807133
Average (Standard dev.)0.0008184878 (±0.021541344)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 262.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39762_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39762_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of human 18_14D C and 1G01 scFv in complex with influen...

EntireName: Structure of human 18_14D C and 1G01 scFv in complex with influenza virus neuraminidase from A/Yunan/DQ001/2016 (H5N6)
Components
  • Complex: Structure of human 18_14D C and 1G01 scFv in complex with influenza virus neuraminidase from A/Yunan/DQ001/2016 (H5N6)
    • Protein or peptide: Neuraminidase
    • Protein or peptide: Light chain of 18_14D scFv
    • Protein or peptide: Heavy chain of 18_14D scFv
    • Protein or peptide: Heavy chain of 1G01 scFv
    • Protein or peptide: Light chain of 1G01 scFv
  • Ligand: CALCIUM ION

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Supramolecule #1: Structure of human 18_14D C and 1G01 scFv in complex with influen...

SupramoleculeName: Structure of human 18_14D C and 1G01 scFv in complex with influenza virus neuraminidase from A/Yunan/DQ001/2016 (H5N6)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Influenza A virus (A/Yunan/DQ001/2016 (H5N6))

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Macromolecule #1: Neuraminidase

MacromoleculeName: Neuraminidase / type: protein_or_peptide / ID: 1
Details: Sequence reference for Influenza A virus (A/Yunan/DQ001/2016 (H5N6)) is not available at the time of biocuration. Current sequence reference is from UniProt ID A0A0K0YAP8.
Number of copies: 1 / Enantiomer: LEVO / EC number: exo-alpha-sialidase
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 42.155621 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RTFLNLTKPL CEVNSWHILS KDNAIRIGED AHILVTREPY LSCDPQGCRM FALSQGTTLR GRHANGTIHD KSPFRALISW EMGQAPSPY NTRVECIGWS STSCHDGISR MSICISGPNN NASAVVWYRG RPVTEIPSWV GNILRTQESE CVCHKGICPV V MTDGPANN ...String:
RTFLNLTKPL CEVNSWHILS KDNAIRIGED AHILVTREPY LSCDPQGCRM FALSQGTTLR GRHANGTIHD KSPFRALISW EMGQAPSPY NTRVECIGWS STSCHDGISR MSICISGPNN NASAVVWYRG RPVTEIPSWV GNILRTQESE CVCHKGICPV V MTDGPANN KAATKIIYFK EGKIQKIEEL QGNAQHIEEC SCYGAAGMIK CVCRDNWKGA NRPIITIDPE MMTHTSKYLC SK ILTDTSR PNDPTNGNCD EPITGGSPDP GVKGFAFLDG ENSWLGRTIS KDSRSGYEML KVPNAETDTQ SGPTSYQLIV NNQ NWSGYS GAFIDYWANK ECFNPCFYVE LIRGRPKEID VLWASNSMVA LCGSRERLGS WSW

UniProtKB: Neuraminidase

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Macromolecule #2: Light chain of 18_14D scFv

MacromoleculeName: Light chain of 18_14D scFv / type: protein_or_peptide / ID: 2
Details: According to author, Entity 2 (Light chain of 18_14D scFV, 216 aa, chain B) and Entity 3 (Heavy chain of 18_14D scFV, 236 aa, chain C) are not expressed as one chain.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.813119 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSVLTQPASV SGSPGQSITI SCTGTSSDVG GYNYVSWYQQ HPGKAPKLMI YDVSKRPSGV SNRFSGSKSG NTASLTISGL QAEDEADYY CSSYTSSSTW VFGGGTKLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String:
QSVLTQPASV SGSPGQSITI SCTGTSSDVG GYNYVSWYQQ HPGKAPKLMI YDVSKRPSGV SNRFSGSKSG NTASLTISGL QAEDEADYY CSSYTSSSTW VFGGGTKLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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Macromolecule #3: Heavy chain of 18_14D scFv

MacromoleculeName: Heavy chain of 18_14D scFv / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.064055 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGSSVKV SCKASGGTFS SYAISWVRQA PGQGLEWMGG IIPIFGTANY AQKFQGRVTI TADESTSTAY MELSSLRSE DTAVYYCARG QLRYFDWPTI PSSYYGMDVW GQGTTVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFPEPVTV ...String:
QVQLVQSGAE VKKPGSSVKV SCKASGGTFS SYAISWVRQA PGQGLEWMGG IIPIFGTANY AQKFQGRVTI TADESTSTAY MELSSLRSE DTAVYYCARG QLRYFDWPTI PSSYYGMDVW GQGTTVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFPEPVTV SWNSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKRVE PKSCDKTH

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Macromolecule #4: Heavy chain of 1G01 scFv

MacromoleculeName: Heavy chain of 1G01 scFv / type: protein_or_peptide / ID: 4
Details: According to author, Entity 4 (Heavy chain of 1G01 scFv, 232 aa, chain E) and Entity 5 (Light chain of 1G01 scFV, 216 aa, chain F) are not expressed as one chain.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.933908 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGR ALRPGGSLRL SCAASGFKFD DYAMSWVRQV PGKGLEFVSG LNWNGDITAY TDSVKGRFTV SRDNAKNSLY LHINSPKPE DTALYYCART SSWGDYTRGP EPKITWYFDL WGRGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT ...String:
EVQLVESGGR ALRPGGSLRL SCAASGFKFD DYAMSWVRQV PGKGLEFVSG LNWNGDITAY TDSVKGRFTV SRDNAKNSLY LHINSPKPE DTALYYCART SSWGDYTRGP EPKITWYFDL WGRGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKRV EPKS

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Macromolecule #5: Light chain of 1G01 scFv

MacromoleculeName: Light chain of 1G01 scFv / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.677273 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DDIQLTQSPS FLSASVGDRI TITCRASQGI DGYLAWYQQR PGKAPNLLIY AASLLQSGVP SRFSGSGYGT EFTLTISSLQ PEDFATYYC QHLDSYPLFT FGPGTKVDIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String:
DDIQLTQSPS FLSASVGDRI TITCRASQGI DGYLAWYQQR PGKAPNLLIY AASLLQSGVP SRFSGSGYGT EFTLTISSLQ PEDFATYYC QHLDSYPLFT FGPGTKVDIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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Macromolecule #7: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / 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: 2.0 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 116206
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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