+Open data
-Basic information
Entry | Database: PDB / ID: 7t01 | ||||||
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Title | SARS-CoV-2 S-RBD + Fab 54042-4 | ||||||
Components |
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Keywords | VIRAL PROTEIN / SARS-CoV-2 / 54042-4 / RBD / Fab / complex / viral protein-immune system | ||||||
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: 2.69 Å | ||||||
Authors | Johnson, N.V. / Mclellan, J.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Cell Rep / Year: 2021 Title: Potent neutralization of SARS-CoV-2 variants of concern by an antibody with an uncommon genetic signature and structural mode of spike recognition. Authors: Kevin J Kramer / Nicole V Johnson / Andrea R Shiakolas / Naveenchandra Suryadevara / Sivakumar Periasamy / Nagarajan Raju / Jazmean K Williams / Daniel Wrapp / Seth J Zost / Lauren M Walker ...Authors: Kevin J Kramer / Nicole V Johnson / Andrea R Shiakolas / Naveenchandra Suryadevara / Sivakumar Periasamy / Nagarajan Raju / Jazmean K Williams / Daniel Wrapp / Seth J Zost / Lauren M Walker / Steven C Wall / Clinton M Holt / Ching-Lin Hsieh / Rachel E Sutton / Ariana Paulo / Rachel S Nargi / Edgar Davidson / Benjamin J Doranz / James E Crowe / Alexander Bukreyev / Robert H Carnahan / Jason S McLellan / Ivelin S Georgiev / Abstract: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages that are more transmissible and resistant to currently approved antibody therapies poses a considerable ...The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages that are more transmissible and resistant to currently approved antibody therapies poses a considerable challenge to the clinical treatment of coronavirus disease (COVID-19). Therefore, the need for ongoing discovery efforts to identify broadly reactive monoclonal antibodies to SARS-CoV-2 is of utmost importance. Here, we report a panel of SARS-CoV-2 antibodies isolated using the linking B cell receptor to antigen specificity through sequencing (LIBRA-seq) technology from an individual who recovered from COVID-19. Of these antibodies, 54042-4 shows potent neutralization against authentic SARS-CoV-2 viruses, including variants of concern (VOCs). A cryoelectron microscopy (cryo-EM) structure of 54042-4 in complex with the SARS-CoV-2 spike reveals an epitope composed of residues that are highly conserved in currently circulating SARS-CoV-2 lineages. Further, 54042-4 possesses uncommon genetic and structural characteristics that distinguish it from other potently neutralizing SARS-CoV-2 antibodies. Together, these findings provide motivation for the development of 54042-4 as a lead candidate to counteract current and future SARS-CoV-2 VOCs. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t01.cif.gz | 82 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t01.ent.gz | 64.5 KB | Display | PDB format |
PDBx/mmJSON format | 7t01.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7t01_validation.pdf.gz | 894.7 KB | Display | wwPDB validaton report |
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Full document | 7t01_full_validation.pdf.gz | 893.3 KB | Display | |
Data in XML | 7t01_validation.xml.gz | 38.5 KB | Display | |
Data in CIF | 7t01_validation.cif.gz | 53.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t0/7t01 ftp://data.pdbj.org/pub/pdb/validation_reports/t0/7t01 | HTTPS FTP |
-Related structure data
Related structure data | 25574MC 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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-Components
#1: Protein | Mass: 22603.408 Da / Num. of mol.: 1 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 |
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#2: Antibody | Mass: 13145.856 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: 11734.157 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex of SARS-CoV-2 S-ECD with 54042-4 Fab / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES | |||||||||||||||
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 | |||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | |||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Sample was monodisperse. All S proteins had 3 Fabs bound. | |||||||||||||||
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: 295 K / Details: -4 force, 3 s blot |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2.5 nm / Nominal defocus min: 1.5 nm |
Image recording | Electron dose: 70 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Particle selection | Num. of particles selected: 478385 |
3D reconstruction | Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 214408 / Symmetry type: POINT |