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	Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries.
ジャーナル・号・ページ	Cell, Vol. 187, Issue 5, Page 1296-1311.e26, Year 2024
掲載日	2024年2月29日
著者	Yu-Xi Tsai / Ning-En Chang / Klaus Reuter / Hao-Ting Chang / Tzu-Jing Yang / Sören von Bülow / Vidhi Sehrawat / Noémie Zerrouki / Matthieu Tuffery / Michael Gecht / Isabell Louise Grothaus / Lucio Colombi Ciacchi / Yong-Sheng Wang / Min-Feng Hsu / Kay-Hooi Khoo / Gerhard Hummer / Shang-Te Danny Hsu / Cyril Hanus / Mateusz Sikora /
PubMed 要旨	Most membrane proteins are modified by covalent addition of complex sugars through N- and O-glycosylation. Unlike proteins, glycans do not typically adopt specific secondary structures and remain ...Most membrane proteins are modified by covalent addition of complex sugars through N- and O-glycosylation. Unlike proteins, glycans do not typically adopt specific secondary structures and remain very mobile, shielding potentially large fractions of protein surface. High glycan conformational freedom hinders complete structural elucidation of glycoproteins. Computer simulations may be used to model glycosylated proteins but require hundreds of thousands of computing hours on supercomputers, thus limiting routine use. Here, we describe GlycoSHIELD, a reductionist method that can be implemented on personal computers to graft realistic ensembles of glycan conformers onto static protein structures in minutes. Using molecular dynamics simulation, small-angle X-ray scattering, cryoelectron microscopy, and mass spectrometry, we show that this open-access toolkit provides enhanced models of glycoprotein structures. Focusing on N-cadherin, human coronavirus spike proteins, and gamma-aminobutyric acid receptors, we show that GlycoSHIELD can shed light on the impact of glycans on the conformation and activity of complex glycoproteins.
リンク	Cell / PubMed:38428397
手法	EM (単粒子)
解像度	4.1 - 6.87 Å
構造データ	33942 7ymt EMDB-33942, PDB-7ymt: Cryo-EM structure of MERS-CoV spike protein, Two RBD-up conformation 2 手法: EM (単粒子) / 解像度: 6.55 Å 33943 7ymv EMDB-33943, PDB-7ymv: Cryo-EM structure of MERS-CoV spike protein, Two RBD-up conformation 1 手法: EM (単粒子) / 解像度: 6.74 Å 33944 7ymw EMDB-33944, PDB-7ymw: Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 4 手法: EM (単粒子) / 解像度: 6.05 Å EMDB-33945: Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 3 手法: EM (単粒子) / 解像度: 6.8 Å 33946 7ymx EMDB-33946, PDB-7ymx: Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 2 手法: EM (単粒子) / 解像度: 4.44 Å 33947 7ymy EMDB-33947, PDB-7ymy: Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 1 手法: EM (単粒子) / 解像度: 4.96 Å 33948 7ymz EMDB-33948, PDB-7ymz: Cryo-EM structure of MERS-CoV spike protein, intermediate conformation 手法: EM (単粒子) / 解像度: 4.39 Å 33949 7yn0 EMDB-33949, PDB-7yn0: Cryo-EM structure of MERS-CoV spike protein, all RBD-down conformation 手法: EM (単粒子) / 解像度: 4.1 Å EMDB-38650: Additional map for SARS-CoV-2 Spike D614G variant, one RBD-up conformation 1 (PDB ID: 7EAZ; EMD-31047). Map was generated from heterogeneous refinement with downsampling in CryoSPARC 手法: EM (単粒子) / 解像度: 6.87 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
由来	human betacoronavirus 2c emc/2012 (ウイルス) Severe acute respiratory syndrome coronavirus 2 (ウイルス)
キーワード	VIRAL PROTEIN / MERS-CoV / Spike / Glycoprotein