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- PDB-9shw: Prefusion-stabilized Nipah virus fusion protein in complex with i... -

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Basic information

Entry
Database: PDB / ID: 9shw
TitlePrefusion-stabilized Nipah virus fusion protein in complex with inhibitory nanobody F112
Components
  • F112 nanobody
  • Fusion glycoprotein F0
KeywordsVIRAL PROTEIN / Fusion protein / antiviral / nanobody
Function / homologymembrane fusion involved in viral entry into host cell / Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesHenipavirus nipahense
Vicugna pacos (alpaca)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsKralova, A. / Hanke, L.
Funding supportEuropean Union, Sweden, 3items
OrganizationGrant numberCountry
European Commission101191794European Union
European Research Council (ERC)101165699European Union
Swedish Research Council2021-01723 Sweden
CitationJournal: To Be Published
Title: Prefusion-stabilized Nipah virus fusion protein in complex with inhibitory nanobody F112
Authors: Kralova, A. / Hanke, L.
History
DepositionAug 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Aa: Fusion glycoprotein F0
Ab: Fusion glycoprotein F0
Ac: Fusion glycoprotein F0
Ba: F112 nanobody
Bb: F112 nanobody
Bc: F112 nanobody


Theoretical massNumber of molelcules
Total (without water)230,5046
Polymers230,5046
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, The trimeric arrangement is consistent with previous paramyxovirus F protein structures. The nanobody:protomer binding ratio of 1:1 was confirmed by the 3D cryo-EM ...Evidence: electron microscopy, The trimeric arrangement is consistent with previous paramyxovirus F protein structures. The nanobody:protomer binding ratio of 1:1 was confirmed by the 3D cryo-EM reconstruction and is supported by prior biochemical characterization of similar complexes.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Fusion glycoprotein F0 / Protein F


Mass: 62510.625 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Henipavirus nipahense / Production host: Homo sapiens (human) / References: UniProt: Q9IH63
#2: Antibody F112 nanobody


Mass: 14323.876 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli BL21 (bacteria)
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Prefusion-stabilized Nipah virus F glycoprotein in complex with the neutralizing F112 nanobodyCOMPLEXall0RECOMBINANT
2Fusion glycoprotein FCOMPLEX#11RECOMBINANT
3F112 nanobodyCOMPLEX#22RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.230279 MDaNO
210.186 MDaNO
310.044 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Henipavirus nipahense3052225
32Henipavirus nipahense3052225
43Vicugna pacos (alpaca)30538
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Escherichia coli (E. coli)562
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1200 mMTrisC4H11NO31
2500 mMSucroseC12H22O111
30.65 mMEDTAC10H16N2O81
SpecimenConc.: 0.24 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 48.28 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
14ISOLDEmodel refinement
15ModelAngelomodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 139202 / Symmetry type: POINT
Atomic model buildingMethod: in silico model
Atomic model buildingSource name: AlphaFold
RefinementCross valid method: NONE

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