Structural analysis of the Spike of the Omicron SARS-COV-2 variant by cryo-EM and implications for immune evasion
Ni, D., Lau, K., Turelli, P., Raclot, C., Beckert, B., Nazarov, S., Pojer, F., Myasnikov, A., Stahlberg, H., Trono, D.(2021) bioRxiv
Experimental Data Snapshot
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
(2021) bioRxiv
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Surface glycoprotein,Fibritin,SARS-CoV-2 S Omicron Spike B.1.1.529 | 1,285 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 0 | ||
UniProt | |||||
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2 | |||||
Entity Groups | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P0DTC2 | ||||
Glycosylation | |||||
Glycosylation Sites: 15 | Go to GlyGen: P0DTC2-1 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD |
Entity ID: 3 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | E, H, M | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT |
Ligands 1 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | AA [auth A] BA [auth A] CA [auth A] DA [auth A] EA [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Task | Software Package | Version |
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MODEL REFINEMENT | PHENIX | |
RECONSTRUCTION | cryoSPARC | 3.3.1 |
Funding Organization | Location | Grant Number |
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Swiss National Science Foundation | Switzerland | -- |