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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Cryo-EM structure of RSV preF in complex with Fab 2.4K | |||||||||
![]() | Sharpened 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 | |||||||||
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![]() | Complex / antibody / fusion protein / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | ![]() positive regulation of syncytium formation by virus / 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 | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
![]() | McCool RS / McLellan JS | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 204 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.7 KB 23.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.3 KB | Display | ![]() |
Images | ![]() | 58.5 KB | ||
Masks | ![]() | 216 MB | ![]() | |
Filedesc metadata | ![]() | 6.6 KB | ||
Others | ![]() ![]() ![]() | 108.4 MB 200.3 MB 200.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8t7aMC 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
File | ![]() | ||||||||||||||||||||
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Annotation | Sharpened 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 | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.94 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map of of prefusion-stabilized RSV F (PR-DM)...
File | emd_41089_additional_1.map | ||||||||||||
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Annotation | Unsharpened 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 |
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Density Histograms |
-Half map: Half map A of prefusion-stabilized RSV F (PR-DM)...
File | emd_41089_half_map_1.map | ||||||||||||
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Annotation | Half 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 |
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Density Histograms |
-Half map: Half map B of prefusion-stabilized RSV F (PR-DM)...
File | emd_41089_half_map_2.map | ||||||||||||
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Annotation | Half 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 |
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Density Histograms |
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Sample components
-Entire : Prefusion-stabilized respiratory syncytial virus in complex with ...
Entire | Name: Prefusion-stabilized respiratory syncytial virus in complex with Fab 2.4K |
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Components |
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-Supramolecule #1: Prefusion-stabilized respiratory syncytial virus in complex with ...
Supramolecule | Name: 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
Supramolecule | Name: Prefusion-stabilized respiratory syncytial virus / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Supramolecule #3: Fab 2.4K
Supramolecule | Name: Fab 2.4K / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Fusion glycoprotein F2
Macromolecule | Name: Fusion glycoprotein F2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 9.498826 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: QNITEEFYQS TCSAVSKGYL SALRTGWYTS VITIELSNIK EIKCNGTDAK VKLIKQELDK YKNAVTELQL LMQSTPAANN RARR UniProtKB: Fusion glycoprotein F0 |
-Macromolecule #2: Fusion glycoprotein F1
Macromolecule | Name: Fusion glycoprotein F1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 48.295859 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #3: 2.4K Fab Heavy Chain
Macromolecule | Name: 2.4K Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.694181 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: QVQLVQSGGE VKKPGASVKV SCKASGYTFT YYGISWVRQA PGQGLEWMGW ISAYNGNTNY EQKFQGRVTM TTDTSTGTAY MELRSLTSD DTAVYYCARD RIVVVTAANY YGLDVWGQGT TVTVSS |
-Macromolecule #4: 2.4K Fab Light Chain
Macromolecule | Name: 2.4K Fab Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 12.447853 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: DIQLTQSPDS LAVSLGERAT INCKSSQSVL YRPNNKNFLA WYQQKPGQPP KLLIYWASTR QSGVPDRFSG SGSGTDFTLT ISSLQAEDV AVYYCQQYHT TPLTFGGGTK VDIK |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / 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 | 3.4 mg/mL | |||||||||
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Buffer | pH: 8 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |