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- EMDB-41089: Cryo-EM structure of RSV preF in complex with Fab 2.4K -

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Basic information

Entry
Database: EMDB / ID: EMD-41089
TitleCryo-EM structure of RSV preF in complex with Fab 2.4K
Map dataSharpened map of of prefusion-stabilized RSV F (PR-DM) complexed with the antigen binding fragment (Fab) from a member of the RSV F public clonotype 2 (2.4K Fab). Sharpened by DeepEMhancer
Sample
  • Complex: Prefusion-stabilized respiratory syncytial virus in complex with Fab 2.4K
    • Complex: Prefusion-stabilized respiratory syncytial virus
      • Protein or peptide: Fusion glycoprotein F2
    • Complex: Fab 2.4K
      • Protein or peptide: 2.4K Fab Heavy Chain
      • Protein or peptide: 2.4K Fab Light Chain
  • Protein or peptide: Fusion glycoprotein F1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsComplex / antibody / fusion protein / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / 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) / Respiratory syncytial virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsMcCool RS / McLellan JS
Funding support United States, 1 items
OrganizationGrant numberCountry
Welch FoundationF-0003-19620604 United States
CitationJournal: J Virol / Year: 2023
Title: Vaccination with prefusion-stabilized respiratory syncytial virus fusion protein elicits antibodies targeting a membrane-proximal epitope.
Authors: Ryan S McCool / Maryam Musayev / Sabrina M Bush / Alexandrine Derrien-Colemyn / Cory M Acreman / Daniel Wrapp / Tracy J Ruckwardt / Barney S Graham / John R Mascola / Jason S McLellan /
Abstract: Respiratory syncytial virus (RSV) is the leading cause of bronchiolitis and pneumonia in infants, infecting all children by age 5. RSV also causes substantial morbidity and mortality in older adults, ...Respiratory syncytial virus (RSV) is the leading cause of bronchiolitis and pneumonia in infants, infecting all children by age 5. RSV also causes substantial morbidity and mortality in older adults, and a vaccine for older adults based on a prefusion-stabilized form of the viral F glycoprotein was recently approved by the FDA. Here, we investigate a set of antibodies that belong to the same public clonotype and were isolated from individuals vaccinated with a prefusion-stabilized RSV F protein. Our results reveal that these antibodies are highly potent and recognize a previously uncharacterized antigenic site on the prefusion F protein. Vaccination with prefusion RSV F proteins appears to boost the elicitation of these neutralizing antibodies, which are not commonly elicited by natural infection.
History
DepositionJun 20, 2023-
Header (metadata) releaseSep 13, 2023-
Map releaseSep 13, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41089.png

Downloads & links

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Map

FileDownload / File: emd_41089.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of of prefusion-stabilized RSV F (PR-DM) complexed with the antigen binding fragment (Fab) from a member of the RSV F public clonotype 2 (2.4K Fab). Sharpened by DeepEMhancer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 384 pix.
= 360.96 Å		0.94 Å/pix.
x 384 pix.
= 360.96 Å		0.94 Å/pix.
x 384 pix.
= 360.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.324
Minimum - Maximum-2.330073 - 2.9766572
Average (Standard dev.)-0.000029696808 (±0.049129527)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 360.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41089_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map of of prefusion-stabilized RSV F (PR-DM)...

Fileemd_41089_additional_1.map
AnnotationUnsharpened map of of prefusion-stabilized RSV F (PR-DM) complexed with the antigen binding fragment (Fab) from a member of the RSV F public clonotype 2 (2.4K Fab).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of prefusion-stabilized RSV F (PR-DM)...

Fileemd_41089_half_map_1.map
AnnotationHalf map A of prefusion-stabilized RSV F (PR-DM) complexed with the antigen binding fragment (Fab) from a member of the RSV F public clonotype 2 (2.4K Fab).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of prefusion-stabilized RSV F (PR-DM)...

Fileemd_41089_half_map_2.map
AnnotationHalf map B of prefusion-stabilized RSV F (PR-DM) complexed with the antigen binding fragment (Fab) from a member of the RSV F public clonotype 2 (2.4K Fab).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Prefusion-stabilized respiratory syncytial virus in complex with ...

EntireName: Prefusion-stabilized respiratory syncytial virus in complex with Fab 2.4K
Components
  • Complex: Prefusion-stabilized respiratory syncytial virus in complex with Fab 2.4K
    • Complex: Prefusion-stabilized respiratory syncytial virus
      • Protein or peptide: Fusion glycoprotein F2
    • Complex: Fab 2.4K
      • Protein or peptide: 2.4K Fab Heavy Chain
      • Protein or peptide: 2.4K Fab Light Chain
  • Protein or peptide: Fusion glycoprotein F1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Prefusion-stabilized respiratory syncytial virus in complex with ...

SupramoleculeName: Prefusion-stabilized respiratory syncytial virus in complex with Fab 2.4K
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3-#4

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Supramolecule #2: Prefusion-stabilized respiratory syncytial virus

SupramoleculeName: Prefusion-stabilized respiratory syncytial virus / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Respiratory syncytial virus A2

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Supramolecule #3: Fab 2.4K

SupramoleculeName: Fab 2.4K / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Fusion glycoprotein F2

MacromoleculeName: Fusion glycoprotein F2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Respiratory syncytial virus / Strain: A2
Molecular weightTheoretical: 9.498826 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QNITEEFYQS TCSAVSKGYL SALRTGWYTS VITIELSNIK EIKCNGTDAK VKLIKQELDK YKNAVTELQL LMQSTPAANN RARR

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: Fusion glycoprotein F1

MacromoleculeName: Fusion glycoprotein F1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Respiratory syncytial virus / Strain: A2
Molecular weightTheoretical: 48.295859 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FLGFLLGVGS AIASGVAVSK VLHLEGEVNK IKSALLSTNK AVVSLSNGVS VLTSKVLDLK NYIDKQLLPI VNKQSCSIPN IETVIEFQQ KNNRLLEITR EFSVNAGVTT PVSTYMLTNS ELLSLINDMP ITNDQKKLMS NNVQIVRQQS YSIMSIIKEE V LAYVVQLP ...String:
FLGFLLGVGS AIASGVAVSK VLHLEGEVNK IKSALLSTNK AVVSLSNGVS VLTSKVLDLK NYIDKQLLPI VNKQSCSIPN IETVIEFQQ KNNRLLEITR EFSVNAGVTT PVSTYMLTNS ELLSLINDMP ITNDQKKLMS NNVQIVRQQS YSIMSIIKEE V LAYVVQLP LYGVIDTPCW KLHTSPLCTT NTKEGSNICL TRTDRGWYCD NAGSVSFFPQ AETCKVQSNR VFCDTMNSLT LP SEVNLCN VDIFNPKYDC KIMTSKTDVS SSVITSLGAI VSCYGKTKCT ASNKNRGIIK TFSNGCDYVS NKGVDTVSVG NTL YYVNKQ EGKSLYVKGE PIINFYDPLV FPSDEFDASI SQVNEKINQS LAFIRKSDEL LGSGYIPEAP RDGQAYVRKD GEWV LLSTF LGRSLEVLFQ GPGHHHHHHH HSAWSHPQFE K

UniProtKB: Fusion glycoprotein F0

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Macromolecule #3: 2.4K Fab Heavy Chain

MacromoleculeName: 2.4K Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.694181 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGGE VKKPGASVKV SCKASGYTFT YYGISWVRQA PGQGLEWMGW ISAYNGNTNY EQKFQGRVTM TTDTSTGTAY MELRSLTSD DTAVYYCARD RIVVVTAANY YGLDVWGQGT TVTVSS

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Macromolecule #4: 2.4K Fab Light Chain

MacromoleculeName: 2.4K Fab Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.447853 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQLTQSPDS LAVSLGERAT INCKSSQSVL YRPNNKNFLA WYQQKPGQPP KLLIYWASTR QSGVPDRFSG SGSGTDFTLT ISSLQAEDV AVYYCQQYHT TPLTFGGGTK VDIK

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration3.4 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
2.0 mMTris base
200.0 mMsodium chlorideNaCl
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm

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Image processing

DetailsPrefusion-stabilized respiratory syncytial virus in complex with Fab 2.4K
Particle selectionNumber selected: 918432
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5c69

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 268139
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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