EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	Structural diversity of the SARS-CoV-2 Omicron spike.
ジャーナル・号・ページ	Mol Cell, Vol. 82, Issue 11, Page 2050-22068.e6, Year 2022
掲載日	2022年6月2日
著者	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 要旨	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.
リンク	Mol Cell / PubMed:35447081 / PubMed Central
手法	EM (単粒子) / X線回折
解像度	2.15 - 4.07 Å
構造データ	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) 手法: EM (単粒子) / 解像度: 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) 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 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) 手法: EM (単粒子) / 解像度: 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) 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 3.87 Å PDB-7tow: Antibody DH1058 Fab fragment bound to SARS-CoV-2 fusion peptide 手法: X-RAY DIFFRACTION / 解像度: 2.15 Å
化合物	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose / N-アセチル-β-D-グルコサミン / N-アセチルグルコサミン ChemComp-CA: Unknown entry / カルシウムジカチオン ChemComp-PO4: PHOSPHATE ION / ホスファ-ト / リン酸塩 ChemComp-HOH: WATER / 水
由来	severe acute respiratory syndrome coronavirus 2 (SARSコロナウイルス2) homo sapiens (ヒト)
キーワード	VIRAL PROTEIN (ウイルスタンパク質) / Omicron Spike protein / SARS-CoV-2 (SARSコロナウイルス2) / variant of concern / 1-up / 3-down / VIRAL PROTEIN/IMMUNE SYSTEM (ウイルス性) / RBD antibody / DH1042 / SARS (重症急性呼吸器症候群) / COVID-19 (新型コロナウイルス感染症 (2019年)) / SARS-CoV-2 2P S ectodomain / IMMUNE SYSTEM (免疫系) / VIRAL PROTEIN-IMMUNE SYSTEM complex (ウイルス性) / Spike / Fusion Protein (融合タンパク質) / SARS-CoV-2 Spike Protein Trimer / IMMUNE SYSTEM/Viral Protein (免疫系) / Antibody (抗体) / Fab fragment / IMMUNE SYSTEM-Viral Protein complex (免疫系)