+Open data
-Basic information
Entry | Database: PDB / ID: 8fu7 | ||||||
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Title | Structure of Covid Spike variant deltaN135 in fully closed form | ||||||
Components | Spike glycoprotein | ||||||
Keywords | VIRAL PROTEIN / Covid Spike / SARS-CoV-2 | ||||||
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 / 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 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.21 Å | ||||||
Authors | Yu, X. / Juraszek, J. / Rutten, L. / Bakkers, M.J.G. / Blokland, S. / Van den Broek, N.J.F. / Verwilligen, A.Y.W. / Abeywickrema, P. / Vingerhoets, J. / Neefs, J. ...Yu, X. / Juraszek, J. / Rutten, L. / Bakkers, M.J.G. / Blokland, S. / Van den Broek, N.J.F. / Verwilligen, A.Y.W. / Abeywickrema, P. / Vingerhoets, J. / Neefs, J. / Bakhash, S.A.M. / Roychoudhury, P. / Greninger, A. / Sharma, S. / Langedijk, J.P.M. | ||||||
Funding support | 1items
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Citation | Journal: PLoS Pathog / Year: 2023 Title: Convergence of immune escape strategies highlights plasticity of SARS-CoV-2 spike. Authors: Xiaodi Yu / Jarek Juraszek / Lucy Rutten / Mark J G Bakkers / Sven Blokland / Jelle M Melchers / Niels J F van den Broek / Annemiek Y W Verwilligen / Pravien Abeywickrema / Johan Vingerhoets ...Authors: Xiaodi Yu / Jarek Juraszek / Lucy Rutten / Mark J G Bakkers / Sven Blokland / Jelle M Melchers / Niels J F van den Broek / Annemiek Y W Verwilligen / Pravien Abeywickrema / Johan Vingerhoets / Jean-Marc Neefs / Shah A Mohamed Bakhash / Pavitra Roychoudhury / Alex Greninger / Sujata Sharma / Johannes P M Langedijk / Abstract: The global spread of the SARS-CoV-2 virus has resulted in emergence of lineages which impact the effectiveness of immunotherapies and vaccines that are based on the early Wuhan isolate. All currently ...The global spread of the SARS-CoV-2 virus has resulted in emergence of lineages which impact the effectiveness of immunotherapies and vaccines that are based on the early Wuhan isolate. All currently approved vaccines employ the spike protein S, as it is the target for neutralizing antibodies. Here we describe two SARS-CoV-2 isolates with unusually large deletions in the N-terminal domain (NTD) of the spike. Cryo-EM structural analysis shows that the deletions result in complete reshaping of the NTD supersite, an antigenically important region of the NTD. For both spike variants the remodeling of the NTD negatively affects binding of all tested NTD-specific antibodies in and outside of the NTD supersite. For one of the variants, we observed a P9L mediated shift of the signal peptide cleavage site resulting in the loss of a disulfide-bridge; a unique escape mechanism with high antigenic impact. Although the observed deletions and disulfide mutations are rare, similar modifications have become independently established in several other lineages, indicating a possibility to become more dominant in the future. The observed plasticity of the NTD foreshadows its broad potential for immune escape with the continued spread of SARS-CoV-2. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fu7.cif.gz | 624.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fu7.ent.gz | 510.5 KB | Display | PDB format |
PDBx/mmJSON format | 8fu7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fu7_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 8fu7_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 8fu7_validation.xml.gz | 90.1 KB | Display | |
Data in CIF | 8fu7_validation.cif.gz | 136.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/8fu7 ftp://data.pdbj.org/pub/pdb/validation_reports/fu/8fu7 | HTTPS FTP |
-Related structure data
Related structure data | 29454MC 8fu8C 8fu9C 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: 132285.828 Da / Num. of mol.: 3 / Mutation: A892P, A942P, D614N,V987P 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: 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
Component | Name: Covid Spike variant deltaN135 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
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 FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1400 nm |
Image recording | Electron dose: 52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: C3 (3 fold cyclic) |
3D reconstruction | Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115817 / Symmetry type: POINT |