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Yorodumi- PDB-7v7j: Cryo-EM structure of SARS-CoV-2 S-Kappa variant (B.1.617.1), dime... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7v7j | |||||||||||||||
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Title | Cryo-EM structure of SARS-CoV-2 S-Kappa variant (B.1.617.1), dimer of S trimer conformation 3 | |||||||||||||||
Components | Spike glycoprotein | |||||||||||||||
Keywords | VIRAL PROTEIN / SARS-CoV-2 / Spike protein | |||||||||||||||
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 / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / 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: 3.4 Å | |||||||||||||||
Authors | Yang, T.J. / Yu, P.Y. / Chang, Y.C. / Hsu, S.T.D. | |||||||||||||||
Funding support | Taiwan, 4items
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Citation | Journal: To Be Published Title: Cryo-EM structure of SARS-CoV-2 S-Kappa variant (B.1.617.1), dimer of S trimer conformation 3 Authors: Yang, T.J. / Yu, P.Y. / Chang, Y.C. / Hsu, S.T.D. | |||||||||||||||
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 | 7v7j.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7v7j.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7v7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7v7j_validation.pdf.gz | 3.6 MB | Display | wwPDB validaton report |
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Full document | 7v7j_full_validation.pdf.gz | 3.6 MB | Display | |
Data in XML | 7v7j_validation.xml.gz | 146.1 KB | Display | |
Data in CIF | 7v7j_validation.cif.gz | 227.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/7v7j ftp://data.pdbj.org/pub/pdb/validation_reports/v7/7v7j | HTTPS FTP |
-Related structure data
Related structure data | 31773MC 7v76C 7v77C 7v78C 7v79C 7v7aC 7v7dC 7v7eC 7v7fC 7v7gC 7v7hC 7v7iC 7v7nC 7v7oC 7v7pC 7v7qC 7v7rC 7v7sC 7v7tC 7v7uC 7v7vC 7v7zC 7v80C 7v81C 7v82C 7v83C 7v84C 7v85C 7v86C 7v87C 7v88C 7v89C 7v8aC 7v8bC 7v8cC 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: 142266.422 Da / Num. of mol.: 6 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: 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: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / Has ligand of interest | N | Has protein modification | 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: SARS-CoV-2 spike glycoprotein / Type: ORGANELLE OR CELLULAR COMPONENT Details: Kappa variant (B.1.617.1), dimer of S trimer conformation 3 Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.54 MDa / Experimental value: YES | ||||||||||||||||||||
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 | ||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Buffer solution | pH: 7.6 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K Details: blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s |
-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 / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109626 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 162.14 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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