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Yorodumi- PDB-7u0p: SARS-Cov2 S protein structure in complex with neutralizing monocl... -
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-Basic information
Entry | Database: PDB / ID: 7u0p | ||||||
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Title | SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-S21F2 | ||||||
Components |
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Keywords | VIRAL PROTEIN / SARS-Cov2 6P spike protein / immune 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 / 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 / membrane fusion / Attachment and Entry / 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 | Severe acute respiratory syndrome coronavirus 2 Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.76 Å | ||||||
Authors | Patel, A. / Ortlund, E. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Adv / Year: 2022 Title: Structural insights for neutralization of Omicron variants BA.1, BA.2, BA.4, and BA.5 by a broadly neutralizing SARS-CoV-2 antibody. Authors: Sanjeev Kumar / Anamika Patel / Lilin Lai / Chennareddy Chakravarthy / Rajesh Valanparambil / Elluri Seetharami Reddy / Kamalvishnu Gottimukkala / Meredith E Davis-Gardner / Venkata ...Authors: Sanjeev Kumar / Anamika Patel / Lilin Lai / Chennareddy Chakravarthy / Rajesh Valanparambil / Elluri Seetharami Reddy / Kamalvishnu Gottimukkala / Meredith E Davis-Gardner / Venkata Viswanadh Edara / Susanne Linderman / Kaustuv Nayak / Kritika Dixit / Pragati Sharma / Prashant Bajpai / Vanshika Singh / Filipp Frank / Narayanaiah Cheedarla / Hans P Verkerke / Andrew S Neish / John D Roback / Grace Mantus / Pawan Kumar Goel / Manju Rahi / Carl W Davis / Jens Wrammert / Sucheta Godbole / Amy R Henry / Daniel C Douek / Mehul S Suthar / Rafi Ahmed / Eric Ortlund / Amit Sharma / Kaja Murali-Krishna / Anmol Chandele / Abstract: In this study, by characterizing several human monoclonal antibodies (mAbs) isolated from single B cells of the COVID-19-recovered individuals in India who experienced ancestral Wuhan strain (WA.1) ...In this study, by characterizing several human monoclonal antibodies (mAbs) isolated from single B cells of the COVID-19-recovered individuals in India who experienced ancestral Wuhan strain (WA.1) of SARS-CoV-2 during early stages of the pandemic, we found a receptor binding domain (RBD)-specific mAb 002-S21F2 that has rare gene usage and potently neutralized live viral isolates of SARS-CoV-2 variants including Alpha, Beta, Gamma, Delta, and Omicron sublineages (BA.1, BA.2, BA.2.12.1, BA.4, and BA.5) with IC ranging from 0.02 to 0.13 μg/ml. Structural studies of 002-S21F2 in complex with spike trimers of Omicron and WA.1 showed that it targets a conformationally conserved epitope on the outer face of RBD (class 3 surface) outside the ACE2-binding motif, thereby providing a mechanistic insights for its broad neutralization activity. The discovery of 002-S21F2 and the broadly neutralizing epitope it targets have timely implications for developing a broad range of therapeutic and vaccine interventions against SARS-CoV-2 variants including Omicron sublineages. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u0p.cif.gz | 717.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u0p.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7u0p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7u0p_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 7u0p_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 7u0p_validation.xml.gz | 118.9 KB | Display | |
Data in CIF | 7u0p_validation.cif.gz | 179.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/7u0p ftp://data.pdbj.org/pub/pdb/validation_reports/u0/7u0p | HTTPS FTP |
-Related structure data
Related structure data | 26262MC 7uplC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 133781.312 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 / Cell line (production host): FreeStyle 293-F / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 #2: Antibody | Mass: 49323.574 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): expi293 / Production host: Homo sapiens (human) #3: Antibody | Mass: 23648.248 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human) #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 | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 297 K / Details: Wait time 20 seconds and blot time 3 seconds |
-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: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 79000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 51 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 3863 |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | |||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2249333 | |||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 129931 / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient | |||||||||||||||||||||||||||||||||||
Refine LS restraints |
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