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Yorodumi- PDB-7tge: SARS-CoV-2 Omicron 1-RBD down Spike Protein Trimer without the P9... -
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-Basic information
Entry | Database: PDB / ID: 7tge | ||||||
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Title | SARS-CoV-2 Omicron 1-RBD down Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron) | ||||||
Components | Spike glycoprotein | ||||||
Keywords | VIRAL PROTEIN / Omicron Spike protein / SARS-CoV-2 / variant of concern / 1-down | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.68 Å | ||||||
Authors | Stalls, V. / Acharya, P. | ||||||
Funding support | United States, 1items
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Citation | Journal: bioRxiv / Year: 2022 Title: Structural diversity of the SARS-CoV-2 Omicron spike. Authors: Sophie M-C Gobeil / Rory Henderson / Victoria Stalls / Katarzyna Janowska / Xiao Huang / Aaron May / Micah Speakman / Esther Beaudoin / Kartik Manne / Dapeng Li / Rob Parks / Maggie Barr / ...Authors: Sophie M-C Gobeil / Rory Henderson / Victoria Stalls / Katarzyna Janowska / Xiao Huang / Aaron May / Micah Speakman / Esther Beaudoin / Kartik Manne / Dapeng Li / Rob Parks / Maggie Barr / Margaret Deyton / Mitchell Martin / Katayoun Mansouri / Robert J Edwards / Gregory D Sempowski / Kevin O Saunders / Kevin Wiehe / Wilton Williams / Bette Korber / Barton F Haynes / Priyamvada Acharya Abstract: Aided by extensive spike protein mutation, the SARS-CoV-2 Omicron variant overtook the previously dominant Delta variant. Spike conformation plays an essential role in SARS-CoV-2 evolution via ...Aided by extensive spike protein mutation, the SARS-CoV-2 Omicron variant overtook the previously dominant Delta variant. Spike conformation plays an essential role in SARS-CoV-2 evolution via changes in receptor binding domain (RBD) and neutralizing antibody epitope presentation affecting virus transmissibility and immune evasion. Here, we determine cryo-EM structures of the Omicron and Delta spikes to understand the conformational impacts of mutations in each. The Omicron spike structure revealed an unusually tightly packed RBD organization with long range impacts that were not observed in the Delta spike. Binding and crystallography revealed increased flexibility at the functionally critical fusion peptide site in the Omicron spike. These results reveal a highly evolved Omicron spike architecture with possible impacts on its high levels of immune evasion and transmissibility. | ||||||
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 | 7tge.cif.gz | 485.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tge.ent.gz | 394.5 KB | Display | PDB format |
PDBx/mmJSON format | 7tge.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tge_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7tge_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7tge_validation.xml.gz | 74.9 KB | Display | |
Data in CIF | 7tge_validation.cif.gz | 114 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/7tge ftp://data.pdbj.org/pub/pdb/validation_reports/tg/7tge | HTTPS FTP |
-Related structure data
Related structure data | 25880MC 7theC 7tlbC 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: 126977.406 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Homo sapiens (human) #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 S-GSAS-Omicron Spike Ectodomain / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.427 MDa / Experimental value: YES |
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: NITROGEN |
-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: 2200 nm / Nominal defocus min: 700 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 215168 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||
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