+Open data
-Basic information
Entry | Database: PDB / ID: 7l3n | ||||||
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Title | SARS-CoV 2 Spike Protein bound to LY-CoV555 | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / Glycoprotein / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information 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 / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å | ||||||
Authors | Goldsmith, J.A. / McLellan, J.S. | ||||||
Citation | Journal: bioRxiv / Year: 2020 Title: LY-CoV555, a rapidly isolated potent neutralizing antibody, provides protection in a non-human primate model of SARS-CoV-2 infection. Authors: Bryan E Jones / Patricia L Brown-Augsburger / Kizzmekia S Corbett / Kathryn Westendorf / Julian Davies / Thomas P Cujec / Christopher M Wiethoff / Jamie L Blackbourne / Beverly A Heinz / ...Authors: Bryan E Jones / Patricia L Brown-Augsburger / Kizzmekia S Corbett / Kathryn Westendorf / Julian Davies / Thomas P Cujec / Christopher M Wiethoff / Jamie L Blackbourne / Beverly A Heinz / Denisa Foster / Richard E Higgs / Deepa Balasubramaniam / Lingshu Wang / Roza Bidshahri / Lucas Kraft / Yuri Hwang / Stefanie Žentelis / Kevin R Jepson / Rodrigo Goya / Maia A Smith / David W Collins / Samuel J Hinshaw / Sean A Tycho / Davide Pellacani / Ping Xiang / Krithika Muthuraman / Solmaz Sobhanifar / Marissa H Piper / Franz J Triana / Jorg Hendle / Anna Pustilnik / Andrew C Adams / Shawn J Berens / Ralph S Baric / David R Martinez / Robert W Cross / Thomas W Geisbert / Viktoriya Borisevich / Olubukola Abiona / Hayley M Belli / Maren de Vries / Adil Mohamed / Meike Dittmann / Marie Samanovic / Mark J Mulligan / Jory A Goldsmith / Ching-Lin Hsieh / Nicole V Johnson / Daniel Wrapp / Jason S McLellan / Bryan C Barnhart / Barney S Graham / John R Mascola / Carl L Hansen / Ester Falconer Abstract: SARS-CoV-2 poses a public health threat for which therapeutic agents are urgently needed. Herein, we report that high-throughput microfluidic screening of antigen-specific B-cells led to the ...SARS-CoV-2 poses a public health threat for which therapeutic agents are urgently needed. Herein, we report that high-throughput microfluidic screening of antigen-specific B-cells led to the identification of LY-CoV555, a potent anti-spike neutralizing antibody from a convalescent COVID-19 patient. Biochemical, structural, and functional characterization revealed high-affinity binding to the receptor-binding domain, ACE2 binding inhibition, and potent neutralizing activity. In a rhesus macaque challenge model, prophylaxis doses as low as 2.5 mg/kg reduced viral replication in the upper and lower respiratory tract. These data demonstrate that high-throughput screening can lead to the identification of a potent antiviral antibody that protects against SARS-CoV-2 infection. ONE SENTENCE SUMMARY: LY-CoV555, an anti-spike antibody derived from a convalescent COVID-19 patient, potently neutralizes SARS-CoV-2 and protects the upper and lower airways of non-human primates ...ONE SENTENCE SUMMARY: LY-CoV555, an anti-spike antibody derived from a convalescent COVID-19 patient, potently neutralizes SARS-CoV-2 and protects the upper and lower airways of non-human primates against SARS-CoV-2 infection. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7l3n.cif.gz | 571 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7l3n.ent.gz | 450.7 KB | Display | PDB format |
PDBx/mmJSON format | 7l3n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/7l3n ftp://data.pdbj.org/pub/pdb/validation_reports/l3/7l3n | HTTPS FTP |
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-Related structure data
Related structure data | 23156MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 141067.672 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 #2: Antibody | | Mass: 24669.691 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Antibody | | Mass: 23097.557 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #4: Polysaccharide | 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: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (recombinant) |
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Buffer solution | pH: 8 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 37.2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60155 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.41 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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