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- EMDB-60572: Complex structure of 60 Fab bound to DS2 prefusion F trimer -

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Basic information

Entry
Database: EMDB / ID: EMD-60572
TitleComplex structure of 60 Fab bound to DS2 prefusion F trimer
Map data
Sample
  • Complex: RSV prefusion protein
    • Protein or peptide: antidody heavy chain
  • Protein or peptide: Fusion glycoprotein F0,Expression tag
  • Protein or peptide: antibody light chain
  • Ligand: water
KeywordsRespiratory syncytial virus / prefusion F protein / DS2 / antibody / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


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 / synthetic construct (others) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsWang X / Ge J / Guo F
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: NPJ Vaccines / Year: 2024
Title: DS2 designer pre-fusion F vaccine induces strong and protective antibody response against RSV infection.
Authors: Yiling Yang / Ruoke Wang / Fenglin Guo / Tian Zhao / Yuqing Lei / Qianqian Yang / Yige Zeng / Ziqing Yang / Tatchapon Ajavavarakula / Ruijie Tan / Mingxi Li / Haodi Dong / Mengyue Niu / ...Authors: Yiling Yang / Ruoke Wang / Fenglin Guo / Tian Zhao / Yuqing Lei / Qianqian Yang / Yige Zeng / Ziqing Yang / Tatchapon Ajavavarakula / Ruijie Tan / Mingxi Li / Haodi Dong / Mengyue Niu / Keyan Bao / Hao Geng / Qining Lv / Qi Zhang / Xuanling Shi / Peng Liu / Jiwan Ge / Xinquan Wang / Linqi Zhang /
Abstract: DS-Cav1, SC-TM, and DS2 are distinct designer pre-fusion F proteins (pre-F) of respiratory syncytial virus (RSV) developed for vaccines. However, their immunogenicity has not been directly compared. ...DS-Cav1, SC-TM, and DS2 are distinct designer pre-fusion F proteins (pre-F) of respiratory syncytial virus (RSV) developed for vaccines. However, their immunogenicity has not been directly compared. In this study, we generated three recombinant vaccines using the chimpanzee adenovirus vector AdC68 to express DS-Cav1, SC-TM, and DS2. All three vaccines elicited robust serum binding and neutralizing antibodies following intramuscular priming and boosting. DS2 induced the strongest antibody responses, followed by SC-TM and DS-Cav1. DS2 also provided strong protection against live RSV challenge. Monoclonal antibodies (mAbs) isolated from long-lived antibody-secreting cells (ASCs) in the bone marrow six months post-immunization with AdC68-DS2 predominantly targeted site Ø as well as site II. One neutralizing antibody against site II, mAb60, conferred strong protection against live RSV infection in mice. These findings highlight the strong ability of the DS2 design in eliciting long-lived antibody responses and guide the development of next-generation RSV vaccines.
History
DepositionJun 18, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60572.png

Downloads & links

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Map

FileDownload / File: emd_60572.map.gz / Format: CCP4 / Size: 115.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 312 pix.
= 335.15 Å		1.07 Å/pix.
x 312 pix.
= 335.15 Å		1.07 Å/pix.
x 312 pix.
= 335.15 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0742 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.6597887 - 2.920618
Average (Standard dev.)0.00075990043 (±0.056547668)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions312312312
Spacing312312312
CellA=B=C: 335.15042 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60572_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_60572_half_map_1.map
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Histogram

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Half map: #1

Fileemd_60572_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : RSV prefusion protein

EntireName: RSV prefusion protein
Components
  • Complex: RSV prefusion protein
    • Protein or peptide: antidody heavy chain
  • Protein or peptide: Fusion glycoprotein F0,Expression tag
  • Protein or peptide: antibody light chain
  • Ligand: water

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Supramolecule #1: RSV prefusion protein

SupramoleculeName: RSV prefusion protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3
Source (natural)Organism: Respiratory syncytial virus A2

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Macromolecule #1: Fusion glycoprotein F0,Expression tag

MacromoleculeName: Fusion glycoprotein F0,Expression tag / type: protein_or_peptide / ID: 1
Details: Sequence reference for Respiratory syncytial virus A2 (1972429) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID C3UPB8.
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 61.26666 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MELLILKANA ITTILTAVTF CFASGQNITE EFYQSTCSAV SKGYLGALRT GWYTSVITIE LSNIKKNKCN GTDAKIKLIK QELDKYKNA VTDLQLLMQS TPATGSGSAI CSGVAVCKVL HLEGEVNKIK SALLSTNKAV VSLSNGVSVL TFKVLDLKNY I DKQLLPIL ...String:
MELLILKANA ITTILTAVTF CFASGQNITE EFYQSTCSAV SKGYLGALRT GWYTSVITIE LSNIKKNKCN GTDAKIKLIK QELDKYKNA VTDLQLLMQS TPATGSGSAI CSGVAVCKVL HLEGEVNKIK SALLSTNKAV VSLSNGVSVL TFKVLDLKNY I DKQLLPIL NKQSCSIPNI ETVIEFQQKN NRLLEITREF SVNAGVTTPV STYMLTNSEL LSLINDMPIT NDQKKLMSNN VQ IVRQQSY SIMCIIKEEV LAYVVQLPLY GVIDTPCWKL HTSPLCTTNT KEGSNICLTR TDRGWYCDNA GSVSFFPQAE TCK VQSNRV FCDTMNSRTL PSEVNLCNVD IFNPKYDCKI MTSKTDVSSS VITSLGAIVS CYGKTKCTAS NKNRGIIKTF SNGC DYVSN KGVDTVSVGN TLYCVNKQEG QSLYVKGEPI INFYDPLVFP SDEFDASISQ VNEKINQSLA FIRKSDELLS AIGGY IPEA PRDGQAYVRK DGEWVLLSTF LGRSLEVLFQ GPGHHHHHHH HSAWSHPQFE KGGGSGGGGS GGSAWSHPQF EKGS

UniProtKB: Fusion glycoprotein F0, Fusion glycoprotein F0

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Macromolecule #2: antibody light chain

MacromoleculeName: antibody light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.305671 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVMTQSPSS LAVSAGEKVT MSCKSSQSVL NSSNQKNYLA WYQQKPGQSP KLLIYWASTR ESGVPDRFTG SGSGTDFTLT ISSVQAEDL AVYYCHQYLY SYTFGGGTRL EIK

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Macromolecule #3: antidody heavy chain

MacromoleculeName: antidody heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.143654 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLKQSGPG LVAPSQSLSI TCTVSGFSLT NYDISWIRQP PGKGLEWLGI IWTGGGTYYN SAFMSRLSIS KDNSKSQVFL EMNSLQTDD TAIYYCVRAG ADYYGSSPLA YWGQGTLVTV SS

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 82401
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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