Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural diversity of the SARS-CoV-2 Omicron spike.
Journal, issue, pages	Mol Cell, Vol. 82, Issue 11, Page 2050-22068.e6, Year 2022
Publish date	Jun 2, 2022
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 / Amanda Eaton / David C Montefiori / Gregory D Sempowski / Kevin O Saunders / Kevin Wiehe / Wilton Williams / Bette Korber / Barton F Haynes / Priyamvada Acharya /
PubMed 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.
External links	Mol Cell / PubMed:35447081 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	2.15 - 4.07 Å
Structure data	25846 7tei EMDB-25846, PDB-7tei: SARS-CoV-2 Omicron 1-RBD up Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron) Method: EM (single particle) / Resolution: 3.4 Å 25865 7tf8 EMDB-25865, PDB-7tf8: SARS-CoV-2 Omicron 3-RBD down Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron) Method: EM (single particle) / Resolution: 3.36 Å 25904 7tht EMDB-25904: CryoEM map of SARS-CoV-2 S protein in complex with Receptor Binding Domain antibody DH1042 PDB-7tht: CryoEM structure of SARS-CoV-2 S protein in complex with Receptor Binding Domain antibody DH1042 Method: EM (single particle) / Resolution: 3.42 Å 25983 7tl1 EMDB-25983, PDB-7tl1: SARS-CoV-2 Omicron 3-RBD down Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron) Method: EM (single particle) / Resolution: 3.5 Å 25984 7tl9 EMDB-25984, PDB-7tl9: SARS-CoV-2 Omicron 1-RBD up Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron) Method: EM (single particle) / Resolution: 3.5 Å 25985 7tla EMDB-25985, PDB-7tla: Down-state locked rS2d SARS-CoV-2 spike ectodomain in the RBD-down conformation, State 1 Method: EM (single particle) / Resolution: 3.13 Å 25987 7tlc EMDB-25987, PDB-7tlc: Down-state locked, S2 stabilized rS2d-HexaPro SARS-CoV-2 spike ectodomain in the RBD-down conformation, State 1 Method: EM (single particle) / Resolution: 2.83 Å 25988 7tld EMDB-25988, PDB-7tld: Down-state locked, S2 stabilized rS2d-HexaPro SARS-CoV-2 spike ectodomain in the RBD-down conformation, State 2 Method: EM (single particle) / Resolution: 2.89 Å 26038 7tou EMDB-26038, PDB-7tou: Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down conformation; consensus state D1 Method: EM (single particle) / Resolution: 3.24 Å 26039 7tov EMDB-26039, PDB-7tov: Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; consensus state D2 Method: EM (single particle) / Resolution: 3.16 Å 26040 7tox EMDB-26040, PDB-7tox: Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down conformation; Subclassification D5 state Method: EM (single particle) / Resolution: 3.62 Å 26041 7toy EMDB-26041, PDB-7toy: Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down conformation; Subclassification D6 state Method: EM (single particle) / Resolution: 3.53 Å 26042 7toz EMDB-26042, PDB-7toz: Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down conformation; Subclassification D7 state Method: EM (single particle) / Resolution: 4.07 Å 26043 7tp0 EMDB-26043, PDB-7tp0: Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down conformation; Subclassification D8 state Method: EM (single particle) / Resolution: 3.57 Å 26045 7tp1 EMDB-26045, PDB-7tp1: Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down conformation; Subclassification D9 state Method: EM (single particle) / Resolution: 3.81 Å 26046 7tp2 EMDB-26046, PDB-7tp2: Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down conformation; Subclassification D10 state Method: EM (single particle) / Resolution: 3.72 Å 26047 7tp7 EMDB-26047, PDB-7tp7: Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; Subclassification D11 state Method: EM (single particle) / Resolution: 3.48 Å 26048 7tp8 EMDB-26048, PDB-7tp8: Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; Subclassification D12 state Method: EM (single particle) / Resolution: 3.4 Å 26049 7tp9 EMDB-26049, PDB-7tp9: Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; Subclassification D13 state Method: EM (single particle) / Resolution: 3.48 Å 26050 7tpa EMDB-26050, PDB-7tpa: Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; Subclassification D14 state Method: EM (single particle) / Resolution: 3.6 Å 26051 7tpc EMDB-26051, PDB-7tpc: Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; Subclassification D15 state Method: EM (single particle) / Resolution: 3.91 Å 26052 7tpe EMDB-26052, PDB-7tpe: Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; Subclassification D16 state Method: EM (single particle) / Resolution: 4.0 Å 26053 7tpf EMDB-26053, PDB-7tpf: Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; Subclassification D17 state Method: EM (single particle) / Resolution: 3.4 Å 26055 7tph EMDB-26055, PDB-7tph: Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 2-RBD-up conformation - D3 Method: EM (single particle) / Resolution: 3.58 Å 26059 7tpl EMDB-26059, PDB-7tpl: Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the M1 conformation, D4 Method: EM (single particle) / Resolution: 3.87 Å PDB-7tow: Antibody DH1058 Fab fragment bound to SARS-CoV-2 fusion peptide Method: X-RAY DIFFRACTION / Resolution: 2.15 Å
Chemicals	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine ChemComp-CA: Unknown entry ChemComp-PO4: PHOSPHATE ION / Phosphate ChemComp-HOH: WATER / Water
Source	severe acute respiratory syndrome coronavirus 2 homo sapiens (human)
Keywords	VIRAL PROTEIN / Omicron Spike protein / SARS-CoV-2 / variant of concern / 1-up / 3-down / VIRAL PROTEIN/IMMUNE SYSTEM / RBD antibody / DH1042 / SARS / COVID-19 / SARS-CoV-2 2P S ectodomain / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex / Spike / Fusion Protein / SARS-CoV-2 Spike Protein Trimer / IMMUNE SYSTEM/Viral Protein / Antibody / Fab fragment / IMMUNE SYSTEM-Viral Protein complex