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- PDB-9wdp: Cyro-EM structure of prefusion RSV fusion glycoprotein in complex... -

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Basic information

Entry
Database: PDB / ID: 9wdp
TitleCyro-EM structure of prefusion RSV fusion glycoprotein in complex with Ziresovir and motavizumab Fab
Components
  • Fusion glycoprotein F0,Fibritin
  • Motavizumab Fab heavy chain
  • Motavizumab Fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Inhibitor / Complex / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / virion component / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane ...symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / virion component / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / identical protein binding / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region
Similarity search - Domain/homology
: / Fusion glycoprotein F0 / Fibritin
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A2
Tequatrovirus T4
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsZhang, W. / Yan, M.R. / Zou, J.J. / Peng, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: PLoS Pathog / Year: 2026
Title: Molecular mechanism of ziresovir targeting the fusion glycoprotein of respiratory syncytial virus.
Authors: Mengrong Yan / Jingjing Zou / Zhao Gao / Haiqing Yuan / Jim Zhen Wu / Gang Zou / Fengjiang Liu / Wei Peng /
Abstract: Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infections in infants and the elderly worldwide. Although prophylactic monoclonal antibodies and RSV vaccines are ...Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infections in infants and the elderly worldwide. Although prophylactic monoclonal antibodies and RSV vaccines are available for preventing severe RSV infection, unmet medical need remains for an effective antiviral agent to treat patients who do not benefit from these interventions. Ziresovir (formerly AK0529) is a potent, selective, and orally bioavailable RSV fusion inhibitor with proved antiviral efficacy and clinical benefits. To understand the molecular mechanism of action, we computationally modeled ziresovir with the RSV fusion (F) protein. Here, we present a cryo-EM structure of the RSV F protein-ziresovir complex, elucidating the molecular interactions underlying the drug binding, revealing ziresovir specifically binds to the central cavity within the metastable prefusion conformation of RSV F protein. Leveraging this structural insight, we engineered site-directed RSV mutants guided by both the cryo-EM binding model and drug-resistant RSV variants for fusion inhibitors identified in vitro, and demonstrated that these resistant viruses do not replicate as efficient as wild-type RSV and indicated a fitness cost for viral escape from drug treatment. Collectively, these findings unveil the structural mechanism of ziresovir-mediated viral inhibition, providing a framework for developing the next-generation RSV fusion inhibitors.
History
DepositionAug 19, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 14, 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,Fibritin
B: Fusion glycoprotein F0,Fibritin
C: Fusion glycoprotein F0,Fibritin
D: Motavizumab Fab heavy chain
E: Motavizumab Fab light chain
F: Motavizumab Fab heavy chain
G: Motavizumab Fab light chain
H: Motavizumab Fab heavy chain
L: Motavizumab Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)339,14810
Polymers338,7089
Non-polymers4401
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Fusion glycoprotein F0,Fibritin / Collar protein / Whisker antigen control protein


Mass: 65513.664 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A2, (gene. exp.) Tequatrovirus T4
Strain: A2 / Gene: wac / Production host: Homo sapiens (human) / References: UniProt: P03420, UniProt: P10104
#2: Antibody Motavizumab Fab heavy chain


Mass: 24284.465 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody Motavizumab Fab light chain


Mass: 23104.639 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Chemical ChemComp-A1EV1 / ~{N}-[(3-azanyloxetan-3-yl)methyl]-2-[1,1-bis(oxidanylidene)-3,5-dihydro-2~{H}-1$l^{6},4-benzothiazepin-4-yl]-6-methyl-quinazolin-4-amine / Ziresovir


Mass: 439.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H25N5O3S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: prefusion RSV fusion glycoprotein in complex with ziresovir and motavizumab Fab
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Human respiratory syncytial virus A211259
31Mus musculus (house mouse)10090
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
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: 2400 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81339 / Symmetry type: POINT
RefinementHighest resolution: 3.27 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311664
ELECTRON MICROSCOPYf_angle_d0.61315814
ELECTRON MICROSCOPYf_dihedral_angle_d7.261548
ELECTRON MICROSCOPYf_chiral_restr0.0421860
ELECTRON MICROSCOPYf_plane_restr0.0061953

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