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- PDB-8z4e: Structure of human 18_14D scFv and 1G01 scFv in complex with infl... -

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Basic information

Entry
Database: PDB / ID: 8z4e
TitleStructure of human 18_14D scFv and 1G01 scFv in complex with influenza virus neuraminidase from A/Yunan/DQ001/2016 (H5N6)
Components
  • (Heavy chain of ...) x 2
  • (Light chain of ...) x 2
  • Neuraminidase
KeywordsVIRAL PROTEIN / influenza virus / neuraminidase / human monoclonal antibody / immunogen
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
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsWang, M. / Peng, Q. / Gao, Y. / Shi, Y.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
B: Light chain of 18_14D scFv
C: Heavy chain of 18_14D scFv
E: Heavy chain of 1G01 scFv
F: Light chain of 1G01 scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,1087
Polymers138,6445
Non-polymers4642
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Antibody , 4 types, 4 molecules BCEF

#2: Antibody Light chain of 18_14D scFv


Mass: 22813.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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.
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Heavy chain of 18_14D scFv


Mass: 25064.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody Heavy chain of 1G01 scFv


Mass: 24933.908 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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.
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody Light chain of 1G01 scFv


Mass: 23677.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars / Non-polymers , 3 types, 3 molecules A

#1: Protein Neuraminidase


Mass: 42155.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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.
Source: (gene. exp.) Influenza A virus / Gene: NA / Production host: Homo sapiens (human) / References: UniProt: A0A0K0YAP8, exo-alpha-sialidase
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Structure of human 18_14D C and 1G01 scFv in complex with influenza virus neuraminidase from A/Yunan/DQ001/2016 (H5N6)
Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Influenza A virus (A/Yunan/DQ001/2016 (H5N6))
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 116206 / Symmetry type: POINT

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