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- EMDB-49520: Focused refinement of the prefusion F glycoprotein ectodomain of ... -

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Entry
Database: EMDB / ID: EMD-49520
TitleFocused refinement of the prefusion F glycoprotein ectodomain of Nipah virus 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 from Nipah virus
KeywordsF ectodomain / prefusion / viral protein / nipah virus
Biological speciesHenipavirus nipahense
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 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
DepositionMar 3, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49520.png

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Map

FileDownload / File: emd_49520.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.0149264 - 1.4752434
Average (Standard dev.)0.00008134268 (±0.019909922)
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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Mask #1

Fileemd_49520_msk_1.map
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Half map: #1

Fileemd_49520_half_map_1.map
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Half map: #2

Fileemd_49520_half_map_2.map
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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 from Nipah virus

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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: all
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 200 KDa

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Macromolecule #1: Fusion glycoprotein from Nipah virus

MacromoleculeName: Fusion glycoprotein from Nipah virus / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Henipavirus nipahense
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

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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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 440004
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

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