7YMX

Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 2

7YMX の概要

• エントリーDOI: 10.2210/pdb7ymx/pdb
• EMDBエントリー: 33946
• 分子名称: Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (4 entities in total)
• 機能のキーワード: mers-cov, spike, glycoprotein, viral protein
• 由来する生物種: Human betacoronavirus 2c EMC/2012
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 462939.55

構造登録者

Hsu, S.T.D.,Chang, N.E.,Weng, Z.W.,Yang, T.J.,Draczkowski, P. (登録日: 2022-07-29, 公開日: 2023-08-09, 最終更新日: 2024-10-23)

主引用文献

Tsai, Y.X.,Chang, N.E.,Reuter, K.,Chang, H.T.,Yang, T.J.,von Bulow, S.,Sehrawat, V.,Zerrouki, N.,Tuffery, M.,Gecht, M.,Grothaus, I.L.,Colombi Ciacchi, L.,Wang, Y.S.,Hsu, M.F.,Khoo, K.H.,Hummer, G.,Hsu, S.D.,Hanus, C.,Sikora, M.
Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries.
Cell, 187:1296-1311.e26, 2024

PubMed Abstract: 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.

PubMed: 38428397
DOI: 10.1016/j.cell.2024.01.034

実験手法

ELECTRON MICROSCOPY (4.44 Å)