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- EMDB-52448: RSV-F postfusion trimer with two 131-2a Fabs bound -

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Basic information

Entry
Database: EMDB / ID: EMD-52448
TitleRSV-F postfusion trimer with two 131-2a Fabs bound
Map dataRSV-F postfusion trimer with two 131-2a Fabs bound
Sample
  • Complex: RSV-F in postfusion conformation in complex with 131-2a Fab
    • Complex: 131-2a Fab
    • Complex: RSV-F
Keywordsantigenic site I / VIRAL PROTEIN
Biological specieshuman respiratory syncytial virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSnijder J
Funding support Netherlands, European Union, 2 items
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 3, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52448.png

Downloads & links

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Map

FileDownload / File: emd_52448.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRSV-F postfusion trimer with two 131-2a Fabs bound
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 240 pix.
= 300. Å		1.25 Å/pix.
x 240 pix.
= 300. Å		1.25 Å/pix.
x 240 pix.
= 300. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.24
Minimum - Maximum-1.289174 - 2.0538208
Average (Standard dev.)0.0006447447 (±0.040928762)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 300.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52448_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52448_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52448_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RSV-F in postfusion conformation in complex with 131-2a Fab

EntireName: RSV-F in postfusion conformation in complex with 131-2a Fab
Components
  • Complex: RSV-F in postfusion conformation in complex with 131-2a Fab
    • Complex: 131-2a Fab
    • Complex: RSV-F

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Supramolecule #1: RSV-F in postfusion conformation in complex with 131-2a Fab

SupramoleculeName: RSV-F in postfusion conformation in complex with 131-2a Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: human respiratory syncytial virus
Molecular weightTheoretical: 213 kDa/nm

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Supramolecule #2: 131-2a Fab

SupramoleculeName: 131-2a Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #4-#5
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: RSV-F

SupramoleculeName: RSV-F / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: human respiratory syncytial virus

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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