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- EMDB-44380: Prefusion F glycoprotein ectodomain of Nipah virus ectodomain in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-44380
TitlePrefusion F glycoprotein ectodomain of Nipah virus ectodomain in complex with DS90 nanobody
Map data
Sample
  • Complex: Prefusion F glycoprotein ectodomain of Nipah virus ectodomain in complex with DS90 nanobody
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: DS90 nanobody
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsF ectodomain / prefusion / viral protein / nipah virus
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytosol
Similarity search - Function
Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase
Similarity search - Domain/homology
Thymidylate synthase
Similarity search - Component
Biological speciesHenipavirus nipahense / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsLow YS / Isaacs A / Modhiran N / Watterson D
Funding support Australia, 1 items
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, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44380.png

Downloads & links

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Map

FileDownload / File: emd_44380.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.8 Å/pix.
x 448 pix.
= 358.4 Å		0.8 Å/pix.
x 448 pix.
= 358.4 Å		0.8 Å/pix.
x 448 pix.
= 358.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.7002999 - 0.9510422
Average (Standard dev.)0.000055230597 (±0.017241325)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 358.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_44380_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_44380_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 : Prefusion F glycoprotein ectodomain of Nipah virus ectodomain in ...

EntireName: Prefusion F glycoprotein ectodomain of Nipah virus ectodomain in complex with DS90 nanobody
Components
  • Complex: Prefusion F glycoprotein ectodomain of Nipah virus ectodomain in complex with DS90 nanobody
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: DS90 nanobody
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Prefusion F glycoprotein ectodomain of Nipah virus ectodomain in ...

SupramoleculeName: Prefusion F glycoprotein ectodomain of Nipah virus ectodomain in complex with DS90 nanobody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 200 KDa

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Macromolecule #1: Fusion glycoprotein F0

MacromoleculeName: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 50.272504 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: ILHYEKLSKI GLVKGVTRKY KIKSNPLTKD IVIKMIPNVS NMSQCTGSVM ENYKTRLNGI LTPIKGALEI YKNNTHDLVG DVRLAGVIM AGVAIGIATA AQITAGVALY EAMKNADNIN KLKSSIESTN EAVVKLQETA EKTVYVLTAL QDYINTNLVP T IDKISCKQ ...String:
ILHYEKLSKI GLVKGVTRKY KIKSNPLTKD IVIKMIPNVS NMSQCTGSVM ENYKTRLNGI LTPIKGALEI YKNNTHDLVG DVRLAGVIM AGVAIGIATA AQITAGVALY EAMKNADNIN KLKSSIESTN EAVVKLQETA EKTVYVLTAL QDYINTNLVP T IDKISCKQ TELSLDLALS KYLSDLLFVF GPNLQDPVSN SMTIQAISQA FGGNYETLLR TLGYATEDFD DLLESDSITG QI IYVDLSS YYIIVRVYFP ILTEIQQAYI QELLPVSFNN DNSEWISIVP NFILVRNTLI SNIEIGFCLI TKRSVICNQD YAT PMTNNM RECLTGSTEK CPRELVVSSH VPRFALSNGV LFANCISVTC QCQTTGRAIS QSGEQTLLMI DNTTCPTAVL GNVI ISLGK YLGSVNYNSE GIAIGPPVFT DKVDISSQIS SMNQSLQQSK DYIKEAQRLL DT

UniProtKB: Thymidylate synthase

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Macromolecule #2: DS90 nanobody

MacromoleculeName: DS90 nanobody / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 13.433862 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
VQLVESGGGL VQAGGSLRLS CAASGRTFSS YVMGWYRQAP GKEREFVARI SWSGGHTHSA DSVKGRFTIS RDNAKNTVYL QMNSLKPDD TAIYYCNAEP TVTGSWFTPG LQSYWGQGTQ VTVSS

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration0.04 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 87.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 40.0 µm / Calibrated magnification: 60000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 25.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio reconstruction, maximum likelihood
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 200640
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 99.7 / Target criteria: Molprobity
Output model

PDB-9b9e:
Prefusion F glycoprotein ectodomain of Nipah virus ectodomain in complex with DS90 nanobody

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