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- EMDB-26562: Cryo-EM structure of Human respiratory syncytial virus F variant ... -
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Open data
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Basic information
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Title | Cryo-EM structure of Human respiratory syncytial virus F variant (construct pXCS847A) | |||||||||
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Function / homology | Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / host cell plasma membrane / virion membrane / plasma membrane / Fusion glycoprotein F0![]() | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
![]() | Lees JA / Ammirati M / Han S | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Rational design of a highly immunogenic prefusion-stabilized F glycoprotein antigen for a respiratory syncytial virus vaccine. Authors: Ye Che / Alexey V Gribenko / Xi Song / Luke D Handke / Kari S Efferen / Kristin Tompkins / Srinivas Kodali / Lorna Nunez / A Krishna Prasad / Lynn M Phelan / Mark Ammirati / Xiaodi Yu / ...Authors: Ye Che / Alexey V Gribenko / Xi Song / Luke D Handke / Kari S Efferen / Kristin Tompkins / Srinivas Kodali / Lorna Nunez / A Krishna Prasad / Lynn M Phelan / Mark Ammirati / Xiaodi Yu / Joshua A Lees / Wei Chen / Lyndsey Martinez / Vidia Roopchand / Seungil Han / Xiayang Qiu / John P DeVincenzo / Kathrin U Jansen / Philip R Dormitzer / Kena A Swanson / ![]() Abstract: Respiratory syncytial virus (RSV) is the leading, global cause of serious respiratory disease in infants and is an important cause of respiratory illness in older adults. No RSV vaccine is currently ...Respiratory syncytial virus (RSV) is the leading, global cause of serious respiratory disease in infants and is an important cause of respiratory illness in older adults. No RSV vaccine is currently available. The RSV fusion (F) glycoprotein is a key antigen for vaccine development, and its prefusion conformation is the target of the most potent neutralizing antibodies. Here, we describe a computational and experimental strategy for designing immunogens that enhance the conformational stability and immunogenicity of RSV prefusion F. We obtained an optimized vaccine antigen after screening nearly 400 engineered F constructs. Through in vitro and in vivo characterization studies, we identified F constructs that are more stable in the prefusion conformation and elicit ~10-fold higher serum-neutralizing titers in cotton rats than DS-Cav1. The stabilizing mutations of the lead construct (847) were introduced onto F glycoprotein backbones of strains representing the dominant circulating genotypes of the two major RSV subgroups, A and B. Immunization of cotton rats with a bivalent vaccine formulation of these antigens conferred complete protection against RSV challenge, with no evidence of disease enhancement. The resulting bivalent RSV prefusion F investigational vaccine has recently been shown to be efficacious against RSV disease in two pivotal phase 3 efficacy trials, one for passive protection of infants by immunization of pregnant women and the second for active protection of older adults by direct immunization. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 78.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.8 KB 22.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.9 KB | Display | ![]() |
Images | ![]() | 125.8 KB | ||
Others | ![]() ![]() | 65.5 MB 65.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ujaMC ![]() 7uj3C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.37 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_26562_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_26562_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Human respiratory syncytial virus F variant (construct pXCS847A) ...
Entire | Name: Human respiratory syncytial virus F variant (construct pXCS847A) with Fabs AM14 and AM22 |
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Components |
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-Supramolecule #1: Human respiratory syncytial virus F variant (construct pXCS847A) ...
Supramolecule | Name: Human respiratory syncytial virus F variant (construct pXCS847A) with Fabs AM14 and AM22 type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: RSV variant (construct pXCS847A) F1
Macromolecule | Name: RSV variant (construct pXCS847A) F1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 45.025391 KDa |
Recombinant expression | Organism: Mammalia (mammals) |
Sequence | String: FLGFLLGVGS ACASGIAVSK VLHLEGEVNK IKSALLSTNK AVVSLSNGVS VLTIKVLDLK NYIDKQLLPI VNKQSCSISN IETVIEFQQ KNNRLLEITR EFSVNAGVTT PVSTYMLTNS ELLSLINDMP ITNDQKKLMS SNVQIVRQQS YSIMSIIKEE V LAYVVQLP ...String: FLGFLLGVGS ACASGIAVSK VLHLEGEVNK IKSALLSTNK AVVSLSNGVS VLTIKVLDLK NYIDKQLLPI VNKQSCSISN IETVIEFQQ KNNRLLEITR EFSVNAGVTT PVSTYMLTNS ELLSLINDMP ITNDQKKLMS SNVQIVRQQS YSIMSIIKEE V LAYVVQLP LYGVIDTPCW KLHTSPLCTT NTKEGSNICL TRTDRGWYCD NAGSVSFFPQ AETCKVQSNR VFCDTMNSLT LP SEVNLCN IDIFNPKYDC KIMTSKTDVS SSVITSLGAI VSCYGKTKCT ASNKNRGIIK TFSNGCDYVS NKGVDTVSVG NTL YYVNKQ EGKSLYVKGE PIINFYDPLV FPSSEFDASI SQVNEKINQS LAFIRKSDEL LSAIGGYIPE APRDGQAYVR KDGE WVLLS TFLGG |
-Macromolecule #2: AM14 Fab heavy chain
Macromolecule | Name: AM14 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 26.231088 KDa |
Recombinant expression | Organism: Mammalia (mammals) |
Sequence | String: EVQLVESGGG VVQPGRSLRL SCAASGFSFS HYAMHWVRQA PGKGLEWVAV ISYDGENTYY ADSVKGRFSI SRDNSKNTVS LQMNSLRPE DTALYYCARD RIVDDYYYYG MDVWGQGATV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String: EVQLVESGGG VVQPGRSLRL SCAASGFSFS HYAMHWVRQA PGKGLEWVAV ISYDGENTYY ADSVKGRFSI SRDNSKNTVS LQMNSLRPE DTALYYCARD RIVDDYYYYG MDVWGQGATV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDG GGSLVPRGSD YK DDDDK |
-Macromolecule #3: AM14 Fab light chain
Macromolecule | Name: AM14 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 23.972656 KDa |
Recombinant expression | Organism: Mammalia (mammals) |
Sequence | String: DIQMTQSPSS LSASVGDRVT ITCQASQDIK KYLNWYHQKP GKVPELLMHD ASNLETGVPS RFSGRGSGTD FTLTISSLQP EDIGTYYCQ QYDNLPPLTF GGGTKVEIKR TVRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAK VQWKVDNALQ S GNSQESVT ...String: DIQMTQSPSS LSASVGDRVT ITCQASQDIK KYLNWYHQKP GKVPELLMHD ASNLETGVPS RFSGRGSGTD FTLTISSLQP EDIGTYYCQ QYDNLPPLTF GGGTKVEIKR TVRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAK VQWKVDNALQ S GNSQESVT EQDSKDSTYS LSSTLTLSKA DYEKHKVYAC EVTHQGLSSP VTKSFNRGEC |
-Macromolecule #4: AM22 Fab heavy chain
Macromolecule | Name: AM22 Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 25.989154 KDa |
Recombinant expression | Organism: Mammalia (mammals) |
Sequence | String: QVQLVQSGAE VKKPGATVKV SCKISGHTLI KLSIHWVRQA PGKGLEWMGG YEGEVDEIFY AQKFQHRLTV IADTATDTVY MELGRLTSD DTAVYFCGTL GVTVTEAGLG IDDYWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String: QVQLVQSGAE VKKPGATVKV SCKISGHTLI KLSIHWVRQA PGKGLEWMGG YEGEVDEIFY AQKFQHRLTV IADTATDTVY MELGRLTSD DTAVYFCGTL GVTVTEAGLG IDDYWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKVEPKSCD GGGSLVPRGS DY KDDDDK |
-Macromolecule #5: AM22 Fab light chain
Macromolecule | Name: AM22 Fab light chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 23.273938 KDa |
Recombinant expression | Organism: Mammalia (mammals) |
Sequence | String: EIVLTQSPGT LSLSPGERAT LSCRASQIVS RNHLAWYQQK PGQAPRLLIF GASSRATGIP VRFSGSGSGT DFTLTINGLA PEDFAVYYC LSSDSSIFTF GPGTKVDFKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String: EIVLTQSPGT LSLSPGERAT LSCRASQIVS RNHLAWYQQK PGQAPRLLIF GASSRATGIP VRFSGSGSGT DFTLTINGLA PEDFAVYYC LSSDSSIFTF GPGTKVDFKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC |
-Macromolecule #6: RSV variant (construct pXCS847A) F2
Macromolecule | Name: RSV variant (construct pXCS847A) F2 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 12.109954 KDa |
Recombinant expression | Organism: Mammalia (mammals) |
Sequence | String: MELPILKTNA ITTILAAVTL CFASSQNITE EFYQSTCSAV SKGYLSALRT GWYTSVITIE LSNIKENKCN GTDAKVKLIK QELDKYKNA VTELQLLMQS TPACNSRARR |
-Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 3 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.1 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY | |||||||||
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 20.0 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |