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- PDB-9u74: Respiratory Syncytial Virus pre-F trimer bound by neutralizing an... -

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Basic information

Entry
Database: PDB / ID: 9u74
TitleRespiratory Syncytial Virus pre-F trimer bound by neutralizing antibody PR306007
Components
  • Fusion glycoprotein F1
  • Fusion glycoprotein F2
  • PR306007 Hight chain protein
  • PR306007 Light chain protein
KeywordsSTRUCTURAL PROTEIN/IMMUNE SYSTEM / RSV / pre-F / neutralizing antibody / IMMUNE SYSTEM (includes antibodies / antigens) / STRUCTURAL 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 / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope ...symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / 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
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesRespiratory syncytial virus A2
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.08 Å
AuthorsZheng, Z. / Zixian, S. / Rui, F. / Yu, G.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271256 China
National Natural Science Foundation of China (NSFC)32300146 China
CitationJournal: PLoS Pathog / Year: 2025
Title: Discovery and molecular mechanism of potent neutralizing antibody from humanized mice with respiratory syncytial virus.
Authors: Zheng Zhang / Rui Feng / Long Zhang / Qi Yang / Xuehua Chen / Xiaoxiao Wang / Cui Nie / Wei Peng / Xiangxi Wang / Ling Zhu / Yu Guo / Zixian Sun /
Abstract: Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infections among infants and older adults, posing a significant threat to global public health. The prophylactic use of ...Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infections among infants and older adults, posing a significant threat to global public health. The prophylactic use of neutralizing antibodies (nAbs) underscores the need to understand elite RSV antibody neutralization mechanisms, which is fundamental for developing next-generation therapies with enhanced potency and broader activity. In this study, we utilized H2L2 transgenic mice encoding human immunoglobulin variable regions for immunization and successfully screened multiple antibodies with significant neutralizing activity using the Beacon Optofluidic system. One of these antibodies, PR306007, exhibited significantly superior broad-spectrum neutralization against both RSV-A and B subgroups. Cryo-electron microscopy (Cryo-EM) structural analysis revealed that PR306007 binds to a unique epitope that overlaps with antigenic sites II and V of the F protein, with its primary binding regions located at the base of the α6 and α7 helices of site II, and residues S173 and N175 of site V. This binding mode offers valuable insights into enhanced neutralization activity and potentially reduces the risk of emerging immune evasive mutants. Furthermore, PR306007 showed potent in vivo antiviral activity against RSV infection and demonstrated good efficacy against both lower and upper respiratory tract infections, making it a promising prophylactic candidate for broad prevention. These findings provide new insights for the future development of RSV vaccines or nAbs.
History
DepositionMar 24, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion glycoprotein F2
B: Fusion glycoprotein F1
C: Fusion glycoprotein F2
D: Fusion glycoprotein F1
E: Fusion glycoprotein F2
F: Fusion glycoprotein F1
G: PR306007 Light chain protein
H: PR306007 Hight chain protein


Theoretical massNumber of molelcules
Total (without water)185,8558
Polymers185,8558
Non-polymers00
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 F2 / F2


Mass: 8758.934 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Respiratory syncytial virus A2 / Production host: Homo sapiens (human) / References: UniProt: P03420
#2: Protein Fusion glycoprotein F1 / F1


Mass: 45028.449 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Respiratory syncytial virus A2 / Production host: Homo sapiens (human) / References: UniProt: P03420
#3: Antibody PR306007 Light chain protein


Mass: 11448.681 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody PR306007 Hight chain protein


Mass: 13044.427 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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

ComponentName: The complex of PR306007 and the RSV A2 pre-F protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Respiratory syncytial virus
Source (recombinant)Organism: Homo sapiens (human)
Details of virusType: SATELLITE
Buffer solutionpH: 7.2
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: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 4.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27206 / Symmetry type: POINT
RefinementHighest resolution: 4.08 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00312474
ELECTRON MICROSCOPYf_angle_d0.62117010
ELECTRON MICROSCOPYf_dihedral_angle_d4.561773
ELECTRON MICROSCOPYf_chiral_restr0.0432100
ELECTRON MICROSCOPYf_plane_restr0.0042145

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