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- PDB-6tys: A potent cross-neutralizing antibody targeting the fusion glycopr... -

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Basic information

Entry
Database: PDB / ID: 6tys
TitleA potent cross-neutralizing antibody targeting the fusion glycoprotein inhibits Nipah virus and Hendra virus infection
Components
  • (5B3 antibody ...) x 2
  • Fusion glycoprotein F0
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Henipavirus / Nipah virus / Hendra virus / fusion glycoprotein / antibody / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / membrane fusion involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / integral component of membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesNipah virus
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsDang, H.V. / Chan, Y.P. / Park, Y.J. / Snijder, J. / Da Silva, S.C. / Vu, B. / Yan, L. / Feng, Y.R. / Rockx, B. / Geisbert, T. / Mire, C.E. / Broder, C.B. / Veesler, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences120553 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2019
Title: An antibody against the F glycoprotein inhibits Nipah and Hendra virus infections.
Authors: Ha V Dang / Yee-Peng Chan / Young-Jun Park / Joost Snijder / Sofia Cheliout Da Silva / Bang Vu / Lianying Yan / Yan-Ru Feng / Barry Rockx / Thomas W Geisbert / Chad E Mire / Christopher C Broder / David Veesler /
Abstract: Nipah virus (NiV) and Hendra virus (HeV) are zoonotic henipaviruses (HNVs) responsible for outbreaks of encephalitis and respiratory illness with fatality rates of 50-100%. No vaccines or licensed ...Nipah virus (NiV) and Hendra virus (HeV) are zoonotic henipaviruses (HNVs) responsible for outbreaks of encephalitis and respiratory illness with fatality rates of 50-100%. No vaccines or licensed therapeutics currently exist to protect humans against NiV or HeV. HNVs enter host cells by fusing the viral and cellular membranes via the concerted action of the attachment (G) and fusion (F) glycoproteins, the main targets of the humoral immune response. Here, we describe the isolation and humanization of a potent monoclonal antibody cross-neutralizing NiV and HeV. Cryo-electron microscopy, triggering and fusion studies show the antibody binds to a prefusion-specific quaternary epitope, conserved in NiV F and HeV F glycoproteins, and prevents membrane fusion and viral entry. This work supports the importance of the HNV prefusion F conformation for eliciting a robust immune response and paves the way for using this antibody for prophylaxis and post-exposure therapy with NiV- and HeV-infected individuals.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Fusion glycoprotein F0
H: 5B3 antibody heavy chain
L: 5B3 antibody light chain
B: Fusion glycoprotein F0
C: 5B3 antibody heavy chain
D: 5B3 antibody light chain
E: Fusion glycoprotein F0
F: 5B3 antibody heavy chain
G: 5B3 antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,41648
Polymers253,4059
Non-polymers8,01139
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area34700 Å2
ΔGint-77 kcal/mol
Surface area88830 Å2

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Components

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Protein/peptide , 1 types, 3 molecules ABE

#1: Protein/peptide Fusion glycoprotein F0 / Protein F


Mass: 59704.781 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nipah virus / Production host: Homo sapiens (human) / References: UniProt: Q9IH63

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5B3 antibody ... , 2 types, 6 molecules HCFLDG

#2: Protein/peptide 5B3 antibody heavy chain


Mass: 13245.752 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Protein/peptide 5B3 antibody light chain


Mass: 11517.844 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Igkv12-98 / Production host: Mus musculus (house mouse)

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Non-polymers , 3 types, 39 molecules

#4: Chemical...
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / N-Acetylglucosamine
#5: Chemical
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Mannose
#6: Chemical ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Mannose

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Details

Has ligand of interestY

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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

Component

Type: COMPLEX

IDNameEntity IDParent-IDSource
1Nipah virus fusion (F) glycoprotein in complex with the 5B3 antibody Fab fragment1, 2, 30MULTIPLE SOURCES
2Fusion glycoprotein F011RECOMBINANT
35B3 antibody2, 31RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Nipah virus121791
23Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Mus musculus (house mouse)10090
Buffer solutionpH: 8
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 FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2Leginon3image acquisition
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38721 / Symmetry type: POINT

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