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- PDB-9b9e: Prefusion F glycoprotein ectodomain of Nipah virus ectodomain in ... -

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Basic information

Entry
Database: PDB / ID: 9b9e
TitlePrefusion F glycoprotein ectodomain of Nipah virus ectodomain in complex with DS90 nanobody
Components
  • DS90 nanobody
  • Fusion glycoprotein F0
KeywordsVIRAL PROTEIN / F ectodomain / prefusion / nipah virus
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesHenipavirus nipahense
Vicugna pacos (alpaca)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsLow, Y.S. / Isaacs, A. / Modhiran, N. / Watterson, D.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1144025 Australia
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: A nanobody-based therapeutic targeting Nipah virus limits viral escape.
Authors: Ariel Isaacs / Guillermo Valenzuela Nieto / Xinghai Zhang / Naphak Modhiran / Jennifer Barr / Nazia Thakur / Yu Shang Low / Rhys H Parry / James B Barnes / Ronald Jara / Johanna Himelreichs ...Authors: Ariel Isaacs / Guillermo Valenzuela Nieto / Xinghai Zhang / Naphak Modhiran / Jennifer Barr / Nazia Thakur / Yu Shang Low / Rhys H Parry / James B Barnes / Ronald Jara / Johanna Himelreichs / Yanfeng Yao / Camila Deride / Barbara Barthou-Gatica / Constanza Salinas-Rebolledo / Pamela Ehrenfeld / Jun Jet Hen / Noah Hayes / Devina Paramitha / Mahali S Morgan / Christopher L D McMillan / Martina L Jones / Trent P Munro / Alexander A Khromykh / Patrick C Reading / Paul R Young / Keith J Chappell / Yi Shi / Dalan Bailey / Glenn A Marsh / Sandra Chiu / Alejandro Rojas-Fernandez / Daniel Watterson /
Abstract: Nipah virus (NiV) and Hendra virus (HeV) are highly pathogenic henipaviruses without approved human vaccines or therapies. Here, we report on a highly potent bispecific therapeutic that combines an ...Nipah virus (NiV) and Hendra virus (HeV) are highly pathogenic henipaviruses without approved human vaccines or therapies. Here, we report on a highly potent bispecific therapeutic that combines an anti-fusion glycoprotein nanobody with an anti-receptor-binding glycoprotein (RBP) antibody to deliver a dual-targeting biologic that is resistant to viral escape. We show that the nanobody, DS90, engages a unique, conserved site within the fusion glycoprotein of NiV and HeV and provides neutralization and complete protection from NiV disease. Bispecific engineering of DS90 with the anti-RBP monoclonal antibody m102.4 results in neutralization, elimination of viral escape and superior protection from NiV disease compared to leading monovalent approaches. These findings carry implications for the development of cross-neutralizing immunotherapies that limit the emergence of henipaviral escape mutants.
History
DepositionApr 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
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Revision 1.0Jun 4, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion glycoprotein F0
B: Fusion glycoprotein F0
C: Fusion glycoprotein F0
D: DS90 nanobody
E: DS90 nanobody
F: DS90 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,77418
Polymers191,1196
Non-polymers2,65412
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Fusion glycoprotein F0 / Protein F


Mass: 50272.504 Da / Num. of mol.: 3 / Fragment: ectodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Henipavirus nipahense / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q9IH63
#2: Antibody DS90 nanobody


Mass: 13433.862 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Cricetulus griseus (Chinese hamster)
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
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: Prefusion F glycoprotein ectodomain of Nipah virus ectodomain in complex with DS90 nanobody
Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.2 MDa / Experimental value: NO
Source (natural)Organism: Henipavirus nipahense
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster)
Buffer solutionpH: 7.4
SpecimenConc.: 0.04 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Calibrated magnification: 60000 X / Nominal defocus max: 25000 nm / Nominal defocus min: 5000 nm / Cs: 2.7 mm / C2 aperture diameter: 40 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER
Image recordingElectron dose: 87.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.3.1particle selection
2SerialEMimage acquisition
4cryoSPARC3.3.1CTF correction
7ISOLDE1.3model fitting
8Coot0.9.8.1model fitting
10cryoSPARC3.3.1initial Euler assignment
11cryoSPARC3.3.1final Euler assignment
12cryoSPARC3.3.1classification
13cryoSPARC3.3.13D reconstruction
14PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 200640 / Symmetry type: POINT
Atomic model buildingB value: 99.7 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Molprobity
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00813758
ELECTRON MICROSCOPYf_angle_d0.92818684
ELECTRON MICROSCOPYf_dihedral_angle_d12.55046
ELECTRON MICROSCOPYf_chiral_restr0.062256
ELECTRON MICROSCOPYf_plane_restr0.0072361

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