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	Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries.
Journal, issue, pages	Cell, Vol. 187, Issue 5, Page 1296-1311.e26, Year 2024
Publish date	Feb 29, 2024
Authors	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 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 ...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.
External links	Cell / PubMed:38428397
Methods	EM (single particle)
Resolution	4.1 - 6.87 Å
Structure data	33942 7ymt EMDB-33942, PDB-7ymt: Cryo-EM structure of MERS-CoV spike protein, Two RBD-up conformation 2 Method: EM (single particle) / Resolution: 6.55 Å 33943 7ymv EMDB-33943, PDB-7ymv: Cryo-EM structure of MERS-CoV spike protein, Two RBD-up conformation 1 Method: EM (single particle) / Resolution: 6.74 Å 33944 7ymw EMDB-33944, PDB-7ymw: Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 4 Method: EM (single particle) / Resolution: 6.05 Å EMDB-33945: Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 3 Method: EM (single particle) / Resolution: 6.8 Å 33946 7ymx EMDB-33946, PDB-7ymx: Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 2 Method: EM (single particle) / Resolution: 4.44 Å 33947 7ymy EMDB-33947, PDB-7ymy: Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 1 Method: EM (single particle) / Resolution: 4.96 Å 33948 7ymz EMDB-33948, PDB-7ymz: Cryo-EM structure of MERS-CoV spike protein, intermediate conformation Method: EM (single particle) / Resolution: 4.39 Å 33949 7yn0 EMDB-33949, PDB-7yn0: Cryo-EM structure of MERS-CoV spike protein, all RBD-down conformation Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 6.87 Å
Chemicals	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose
Source	human betacoronavirus 2c emc/2012 Severe acute respiratory syndrome coronavirus 2
Keywords	VIRAL PROTEIN / MERS-CoV / Spike / Glycoprotein