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- PDB-9nz0: Cryo-EM structure of vaccine elicited antibody 22F5 bound to the ... -

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Basic information

Entry
Database: PDB / ID: 9nz0
TitleCryo-EM structure of vaccine elicited antibody 22F5 bound to the post-fusion conformation of the LayV-F glycoprotein
Components
  • 22F5 Heavy Chain
  • 22F5 Kappa Light Chain
  • Fusion glycoprotein F0
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / Henipavirus / Langya virus / vaccine-elicited antibody / DII domain / shrew-origin / 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: 3.31 Å
AuthorsKumar, U. / May, A. / 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: To Be Published
Title: Structural and Antigenic Characterization of Novel and Diverse Henipavirus Glycoproteins
Authors: May, A.J. / Lella, M. / Lindenberger, J. / Berkman, A. / Kumar, U. / Haynes, B.F. / Acharya, P.
History
DepositionMar 31, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2026Provider: 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: 22F5 Heavy Chain
E: 22F5 Kappa Light Chain
F: 22F5 Heavy Chain
G: 22F5 Kappa Light Chain
H: 22F5 Kappa Light Chain
I: 22F5 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)328,29315
Polymers326,9669
Non-polymers1,3276
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: 61468.840 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Langya virus / Production host: Homo sapiens (human) / References: UniProt: A0AAX3C923
#2: 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 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.: 6
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

Component
IDNameTypeEntity IDParent-IDSource
1Complex of Langya virus F protein trimer with 22F5 fabCOMPLEX#1-#30MULTIPLE SOURCES
2Langya virus F proteinCOMPLEX#11RECOMBINANT
322F5 fabCOMPLEX#2-#31NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Langya virus2971765
33Mus musculus (house mouse)10090
Source (recombinant)Organism: Homo sapiens (human)
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

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: 2800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 59.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 271130 / Symmetry type: POINT

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