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- PDB-9hvw: Respiratory Syncytial Virus Fusion protein in the postfusion conf... -

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Basic information

Entry
Database: PDB / ID: 9hvw
TitleRespiratory Syncytial Virus Fusion protein in the postfusion conformation in complex with monoclonal antibody 131-2a Fab
Components
  • 131-2a heavy chain
  • 131-2a light chain
  • Fusion glycoprotein F0
  • Fusion glycoprotein F1,Probable N-acetylmuramidase
KeywordsVIRAL PROTEIN / antigenic site I
Function / homology
Function and homology information


peptidoglycan N-acetylglucosaminidase activity / symbiont-mediated induction of syncytium formation / amidase activity / Translation of respiratory syncytial virus mRNAs / division septum assembly / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry ...peptidoglycan N-acetylglucosaminidase activity / symbiont-mediated induction of syncytium formation / amidase activity / Translation of respiratory syncytial virus mRNAs / division septum assembly / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / cell wall organization / lysozyme / lysozyme activity / killing of cells of another organism / entry receptor-mediated virion attachment to host cell / defense response to bacterium / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
: / Lysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / LysM domain
Similarity search - Domain/homology
Probable N-acetylmuramidase / Fusion glycoprotein F0
Similarity search - Component
Biological specieshuman respiratory syncytial virus
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSnijder, J.
Funding support Netherlands, European Union, 2items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
European Research Council (ERC)European Union
CitationJournal: ACS Infect Dis / Year: 2025
Title: Structural Basis for Postfusion-Specific Binding to the Respiratory Syncytial Virus F Protein by the Canonical Antigenic Site I Antibody 131-2a.
Authors: Weiwei Peng / Marta Šiborová / Xuesheng Wu / Wenjuan Du / Douwe Schulte / Matti F Pronker / Cornelis A M de Haan / Joost Snijder /
Abstract: The respiratory syncytial virus (RSV) fusion (F) protein is a major target of antiviral antibodies following natural infection or vaccination and is responsible for mediating fusion between the viral ...The respiratory syncytial virus (RSV) fusion (F) protein is a major target of antiviral antibodies following natural infection or vaccination and is responsible for mediating fusion between the viral envelope and the host membrane. The fusion process is driven by a large-scale conformational change in F, switching irreversibly from the metastable prefusion state to the stable postfusion conformation. Previous research has identified six distinct antigenic sites in RSV-F, termed sites Ø, I, II, III, IV, and V. Of these, only antigenic site I is fully specific to the postfusion conformation of F. A monoclonal antibody 131-2a that specifically targets postfusion F has been widely used as a research tool to probe for postfusion F and to define antigenic site I in serological studies, yet its sequence and precise epitope have remained unknown. Here, we use mass spectrometry-based sequencing of 131-2a to reverse engineer a recombinant product and study the epitope to define antigenic site I with molecular detail, revealing the structural basis for the antibody's specificity toward postfusion RSV-F.
History
DepositionJan 2, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.2Aug 20, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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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: Fusion glycoprotein F1,Probable N-acetylmuramidase
E: Fusion glycoprotein F1,Probable N-acetylmuramidase
F: Fusion glycoprotein F1,Probable N-acetylmuramidase
H: 131-2a heavy chain
L: 131-2a light chain


Theoretical massNumber of molelcules
Total (without water)219,0868
Polymers219,0868
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Fusion glycoprotein F0


Mass: 8930.087 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human respiratory syncytial virus / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P03420
#2: Protein Fusion glycoprotein F1,Probable N-acetylmuramidase / F1 / Autolysin / Lysozyme / Peptidoglycan hydrolase


Mass: 55751.020 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human respiratory syncytial virus / Gene: acmA, llmg_0280 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P03420, UniProt: A2RHZ5, lysozyme
#3: Antibody 131-2a heavy chain


Mass: 13162.569 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Antibody 131-2a light chain


Mass: 11880.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / 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: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1RSV-F in postfusion conformation in complex with 131-2a FabCOMPLEXall0RECOMBINANT
2131-2a FabCOMPLEX#3-#41RECOMBINANT
3RSV-FCOMPLEX#1-#21RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
11262 kDa/nmNO
2149 kDa/nmNO
31213 kDa/nmNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21human respiratory syncytial virus11250
32Mus musculus (house mouse)10090
43human respiratory syncytial virus11250
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Cricetulus griseus (Chinese hamster)10029
32Homo sapiens (human)9606
43Cricetulus griseus (Chinese hamster)10029
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: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 394000 / Symmetry type: POINT

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