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- PDB-7s6l: J08 fragment antigen binding in complex with SARS-CoV-2-6P-Mut7 S... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7s6l | |||||||||
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Title | J08 fragment antigen binding in complex with SARS-CoV-2-6P-Mut7 S protein (conformation 3) | |||||||||
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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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ozorowski, G. / Torres, J.L. / Ward, A.B. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights of a highly potent pan-neutralizing SARS-CoV-2 human monoclonal antibody. Authors: Jonathan L Torres / Gabriel Ozorowski / Emanuele Andreano / Hejun Liu / Jeffrey Copps / Giulia Piccini / Lorena Donnici / Matteo Conti / Cyril Planchais / Delphine Planas / Noemi Manganaro / ...Authors: Jonathan L Torres / Gabriel Ozorowski / Emanuele Andreano / Hejun Liu / Jeffrey Copps / Giulia Piccini / Lorena Donnici / Matteo Conti / Cyril Planchais / Delphine Planas / Noemi Manganaro / Elisa Pantano / Ida Paciello / Piero Pileri / Timothée Bruel / Emanuele Montomoli / Hugo Mouquet / Olivier Schwartz / Claudia Sala / Raffaele De Francesco / Ian A Wilson / Rino Rappuoli / Andrew B Ward / ![]() ![]() ![]() Abstract: As the coronavirus disease 2019 (COVID-19) pandemic continues, there is a strong need for highly potent monoclonal antibodies (mAbs) that are resistant against severe acute respiratory syndrome ...As the coronavirus disease 2019 (COVID-19) pandemic continues, there is a strong need for highly potent monoclonal antibodies (mAbs) that are resistant against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VoCs). Here, we evaluate the potency of the previously described mAb J08 against these variants using cell-based assays and delve into the molecular details of the binding interaction using cryoelectron microscopy (cryo-EM) and X-ray crystallography. We show that mAb J08 has low nanomolar affinity against most VoCs and binds high on the receptor binding domain (RBD) ridge, away from many VoC mutations. These findings further validate the phase II/III human clinical trial underway using mAb J08 as a monoclonal therapy. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 562.5 KB | Display | ![]() |
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PDB format | ![]() | 464.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 24879MC ![]() 7s6iC ![]() 7s6jC ![]() 7s6kC ![]() 7sbuC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | ![]() Mass: 141328.359 Da / Num. of mol.: 3 Mutation: R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: S, 2 / Cell line (production host): HEK293F / Production host: ![]() ![]() #2: Antibody | | Mass: 13961.632 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Antibody | | Mass: 11252.522 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ![]() Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / ![]() Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: J08 fragment antigen binding in complex with SARS-2-CoV-6P-Mut7 S protein Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES | ||||||||||||||||||||
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Molecular weight | Value: 0.59 MDa / Experimental value: NO | ||||||||||||||||||||
Buffer solution | pH: 8 / Details: Detergent added shortly before freezing | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | ||||||||||||||||||||
Vitrification![]() | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 3 s blot time |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 12.5 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 50 |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | |||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() | |||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43511 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | |||||||||||||||||||||||||||||||||||
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