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- PDB-9nz2: Cryo-EM structure of antibody 22F5 in complex with pre-fusion sta... -

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Basic information

Entry
Database: PDB / ID: 9nz2
TitleCryo-EM structure of antibody 22F5 in complex with pre-fusion stabilized LayV-F
Components
  • Antibody 22F5 Heavy Chain
  • Antibody 22F5 Kappa Light Chain
  • Fusion glycoprotein F0
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / Langya virus / parahenipavirus / cross-reactive / DII domain / ANTIVIRAL PROTEIN / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homologyPrecursor 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 speciesLangya virus
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.46 Å
AuthorsMay, A.J. / Kumar, U. / Acharya, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: bioRxiv / Year: 2025
Title: Structural and antigenic characterization of novel and diverse Henipavirus glycoproteins.
Authors: May, A.J. / Lella, M. / Lindenberger, J. / Berkman, A. / Kumar, U. / Dutta, M. / Barr, M. / Parks, R. / Lu, X. / Berry, M. / Newman, A. / Huang, X. / Song, K. / Ilevbare, V. / Sammour, S. / ...Authors: May, A.J. / Lella, M. / Lindenberger, J. / Berkman, A. / Kumar, U. / Dutta, M. / Barr, M. / Parks, R. / Lu, X. / Berry, M. / Newman, A. / Huang, X. / Song, K. / Ilevbare, V. / Sammour, S. / Park, C.S. / Adhikari, R.D. / Devkota, P. / Janowska, K. / Liu, Y. / Scapellato, G. / Spence, T.N. / Mansouri, K. / Wiehe, K. / Edwards, R.J. / Saunders, K.O. / Haynes, B.F. / Acharya, P.
History
DepositionMar 31, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Primary map / Data content type: Primary map / 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: Antibody 22F5 Heavy Chain
E: Antibody 22F5 Kappa Light Chain
F: Antibody 22F5 Heavy Chain
G: Antibody 22F5 Kappa Light Chain
H: Antibody 22F5 Kappa Light Chain
I: Antibody 22F5 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)327,73812
Polymers327,0749
Non-polymers6643
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Fusion glycoprotein F0


Mass: 61504.918 Da / Num. of mol.: 3 / Mutation: G99C, I109C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Langya virus / Production host: Homo sapiens (human) / References: UniProt: A0AAX3C923
#2: Antibody Antibody 22F5 Heavy Chain


Mass: 23195.980 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody Antibody 22F5 Kappa Light Chain


Mass: 24323.928 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: 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.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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 interestN
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: 22F5 Antibody Fab bound to pre-fusion stabilized Langya virus fusion protein
Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS TUNDRA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 30.72 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 245019 / Symmetry type: POINT

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