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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, Z. / Zixian, S. / Rui, F. / Yu, G.
History
DepositionMar 24, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 12, 2025Provider: 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 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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