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- EMDB-40095: 17B10 fab in complex with up-RBD of SARS-CoV-2 Spike G614 trimer -
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Open data
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Basic information
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Title | 17B10 fab in complex with up-RBD of SARS-CoV-2 Spike G614 trimer | |||||||||
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Function / homology | ![]() Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Kwon HJ / Zhang J / Kosikova M / Tang WC / Rodriguez UO / Peng HQ / Meseda CA / Pedro CL / Schmeisser F / Lu JM ...Kwon HJ / Zhang J / Kosikova M / Tang WC / Rodriguez UO / Peng HQ / Meseda CA / Pedro CL / Schmeisser F / Lu JM / Zhou B / Davis CT / Wentworth DE / Chen WH / Shriver MC / Pasetti MF / Weir JP / Chen B / Xie H | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Distinct in vitro and in vivo neutralization profiles of monoclonal antibodies elicited by the receptor binding domain of the ancestral SARS-CoV-2. Authors: Hyung J Kwon / Jun Zhang / Matina Kosikova / Weichun Tang / Uriel Ortega-Rodriguez / Hanqin Peng / Clement A Meseda / Cyntia L Pedro / Falko Schmeisser / Jianming Lu / Insung Kang / Bin Zhou ...Authors: Hyung J Kwon / Jun Zhang / Matina Kosikova / Weichun Tang / Uriel Ortega-Rodriguez / Hanqin Peng / Clement A Meseda / Cyntia L Pedro / Falko Schmeisser / Jianming Lu / Insung Kang / Bin Zhou / Charles T Davis / David E Wentworth / Wilbur H Chen / Mallory C Shriver / Robin S Barnes / Marcela F Pasetti / Jerry P Weir / Bing Chen / Hang Xie / ![]() Abstract: Broadly neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are sought to curb coronavirus disease 2019 (COVID-19) infections. Here we produced and ...Broadly neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are sought to curb coronavirus disease 2019 (COVID-19) infections. Here we produced and characterized a set of mouse monoclonal antibodies (mAbs) specific for the ancestral SARS-CoV-2 receptor binding domain (RBD). Two of them, 17A7 and 17B10, were highly potent in microneutralization assay with 50% inhibitory concentration (IC ) ≤135 ng/mL against infectious SARS-CoV-2 variants, including G614, Alpha, Beta, Gamma, Delta, Epsilon, Zeta, Kappa, Lambda, B.1.1.298, B.1.222, B.1.5, and R.1. Both mAbs (especially 17A7) also exhibited strong in vivo efficacy in protecting K18-hACE2 transgenic mice from the lethal infection with G614, Alpha, Beta, Gamma, and Delta viruses. Structural analysis indicated that 17A7 and 17B10 target the tip of the receptor binding motif in the RBD-up conformation. A third RBD-reactive mAb (3A6) although escaped by Beta and Gamma, was highly effective in cross-neutralizing Delta and Omicron BA.1 variants in vitro and in vivo. In competition experiments, antibodies targeting epitopes similar to these 3 mAbs were rarely enriched in human COVID-19 convalescent sera or postvaccination sera. These results are helpful to inform new antibody/vaccine design and these mAbs can be useful tools for characterizing SARS-CoV-2 variants and elicited antibody responses. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 362.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.6 KB 19.6 KB | Display Display | ![]() |
Images | ![]() | 39.4 KB | ||
Others | ![]() ![]() | 384.9 MB 385.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8gjnMC ![]() 8gjmC 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: 0.825 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_40095_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_40095_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : 17B10 fab in complex with up-RBD of SARS-CoV-2 Spike G614 trimer
Entire | Name: 17B10 fab in complex with up-RBD of SARS-CoV-2 Spike G614 trimer |
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Components |
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-Supramolecule #1: 17B10 fab in complex with up-RBD of SARS-CoV-2 Spike G614 trimer
Supramolecule | Name: 17B10 fab in complex with up-RBD of SARS-CoV-2 Spike G614 trimer type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3 Details: 17B10 fab in complex with up-RBD of SARS-CoV-2 Spike G614 trimer |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 100 KDa |
-Macromolecule #1: Heavy chain of 17B10 Fab
Macromolecule | Name: Heavy chain of 17B10 Fab / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 15.353094 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MGWSWIFLFL LSGTAGVLSE VQLQQSGPEL VKPGASVRIS CKTSGYTFTE YSMFWVKQSH GQSLEWIGGI NPNDDSTTYK QNFKGKATL TVDKSSSTAF MELRSLTSED SAVYYCTRDR YDGRVVDFWG QGTTLTVSS |
-Macromolecule #2: Light chain of 17B10 Fab
Macromolecule | Name: Light chain of 17B10 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 14.090899 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MRVPAHVFGF LLLWFPGTRC DIQMTQSPSS LSASLGERVS LICRASQEIS GYLSWLQQKP DGTIKRLIYA ASTLDSGVPK RFSGSRSGS EYSLTISSPE SEDFADYYCL QYASYPWTFG GGTKLEIK |
-Macromolecule #3: Spike protein S2'
Macromolecule | Name: Spike protein S2' / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 22.218936 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVEGFNCYFP L QSYGFQPT ...String: TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVEGFNCYFP L QSYGFQPT NGVGYQPYRV VVLSFELLHA PATVCGPKKS |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 1 / 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 | 1 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / 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 K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.442 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Protocol: AB INITIO MODEL |
Output model | ![]() PDB-8gjn: |