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Yorodumi- PDB-6zp1: Structure of SARS-CoV-2 Spike Protein Trimer (K986P, V987P, singl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zp1 | |||||||||||||||
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Title | Structure of SARS-CoV-2 Spike Protein Trimer (K986P, V987P, single Arg S1/S2 cleavage site) in Closed State | |||||||||||||||
Components | Spike glycoprotein | |||||||||||||||
Keywords | VIRAL PROTEIN / coronavirus / SARS-CoV-2 / Spike protein / S protein / S antigen / COVID-19 / receptor binding / membrane fusion / vaccine design | |||||||||||||||
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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / 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 | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||
Authors | Xiong, X. / Qu, K. / Scheres, S.H.W. / Briggs, J.A.G. | |||||||||||||||
Funding support | United Kingdom, European Union, Germany, 4items
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Citation | Journal: Nat Struct Mol Biol / Year: 2020 Title: A thermostable, closed SARS-CoV-2 spike protein trimer. Authors: Xiaoli Xiong / Kun Qu / Katarzyna A Ciazynska / Myra Hosmillo / Andrew P Carter / Soraya Ebrahimi / Zunlong Ke / Sjors H W Scheres / Laura Bergamaschi / Guinevere L Grice / Ying Zhang / / ...Authors: Xiaoli Xiong / Kun Qu / Katarzyna A Ciazynska / Myra Hosmillo / Andrew P Carter / Soraya Ebrahimi / Zunlong Ke / Sjors H W Scheres / Laura Bergamaschi / Guinevere L Grice / Ying Zhang / / James A Nathan / Stephen Baker / Leo C James / Helen E Baxendale / Ian Goodfellow / Rainer Doffinger / John A G Briggs / Abstract: The spike (S) protein of SARS-CoV-2 mediates receptor binding and cell entry and is the dominant target of the immune system. It exhibits substantial conformational flexibility. It transitions from ...The spike (S) protein of SARS-CoV-2 mediates receptor binding and cell entry and is the dominant target of the immune system. It exhibits substantial conformational flexibility. It transitions from closed to open conformations to expose its receptor-binding site and, subsequently, from prefusion to postfusion conformations to mediate fusion of viral and cellular membranes. S-protein derivatives are components of vaccine candidates and diagnostic assays, as well as tools for research into the biology and immunology of SARS-CoV-2. Here we have designed mutations in S that allow the production of thermostable, disulfide-bonded S-protein trimers that are trapped in the closed, prefusion state. Structures of the disulfide-stabilized and non-disulfide-stabilized proteins reveal distinct closed and locked conformations of the S trimer. We demonstrate that the designed, thermostable, closed S trimer can be used in serological assays. This protein has potential applications as a reagent for serology, virology and as an immunogen. | |||||||||||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6zp1.cif.gz | 559.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zp1.ent.gz | 462.7 KB | Display | PDB format |
PDBx/mmJSON format | 6zp1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zp1_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6zp1_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6zp1_validation.xml.gz | 82 KB | Display | |
Data in CIF | 6zp1_validation.cif.gz | 124.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/6zp1 ftp://data.pdbj.org/pub/pdb/validation_reports/zp/6zp1 | HTTPS FTP |
-Related structure data
Related structure data | 11333MC 6zoxC 6zoyC 6zozC 6zp0C 6zp2C 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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-Components
#1: Protein | Mass: 138278.828 Da / Num. of mol.: 3 / Mutation: K986P, V987P, Single Arg S1/S2 cleavage site Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Variant: K986P / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 #2: 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 #3: 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: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: SARS-CoV-2 Spike Protein Trimer / Type: COMPLEX / Details: K986P, V987P, Single Arg S1/S2 cleavage site / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: WIV-04 | |||||||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: Expi293 / Plasmid: pCDNA3.1 | |||||||||||||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid type: C-flat-2/2 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K |
-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 magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4563 |
EM imaging optics | Energyfilter name: GIF Quantum LS |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / 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: 3376871 / Details: template picking | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59857 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 117 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: correlation coefficient | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6VXX Pdb chain-ID: A | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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