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	Factors affecting macromolecule orientations in thin films formed in cryo-EM.
Journal, issue, pages	Acta Crystallogr D Struct Biol, Vol. 80, Issue Pt 7, Page 535-550, Year 2024
Publish date	Jul 1, 2024
Authors	Swati Yadav / Kutti R Vinothkumar /
PubMed Abstract	The formation of a vitrified thin film embedded with randomly oriented macromolecules is an essential prerequisite for cryogenic sample electron microscopy. Most commonly, this is achieved using the ...The formation of a vitrified thin film embedded with randomly oriented macromolecules is an essential prerequisite for cryogenic sample electron microscopy. Most commonly, this is achieved using the plunge-freeze method first described nearly 40 years ago. Although this is a robust method, the behaviour of different macromolecules shows great variation upon freezing and often needs to be optimized to obtain an isotropic, high-resolution reconstruction. For a macromolecule in such a film, the probability of encountering the air-water interface in the time between blotting and freezing and adopting preferred orientations is very high. 3D reconstruction using preferentially oriented particles often leads to anisotropic and uninterpretable maps. Currently, there are no general solutions to this prevalent issue, but several approaches largely focusing on sample preparation with the use of additives and novel grid modifications have been attempted. In this study, the effect of physical and chemical factors on the orientations of macromolecules was investigated through an analysis of selected well studied macromolecules, and important parameters that determine the behaviour of proteins on cryo-EM grids were revealed. These insights highlight the nature of the interactions that cause preferred orientations and can be utilized to systematically address orientation bias for any given macromolecule and to provide a framework to design small-molecule additives to enhance sample stability and behaviour.
External links	Acta Crystallogr D Struct Biol / PubMed:38935342 / PubMed Central
Methods	EM (single particle)
Resolution	2.4 - 3.7 Å
Structure data	37952 EMDB entry, No image 8wzh EMDB-37952, PDB-8wzh: Human erythrocyte catalase with SLS as additive during cryo-EM grid preparation Method: EM (single particle) / Resolution: 3.7 Å 37953 EMDB entry, No image 8wzi EMDB-37953, PDB-8wzi: One RBD up state of Spike glycoprotein, SARS-CoV-2 Method: EM (single particle) / Resolution: 3.0 Å 37954 EMDB entry, No image 8wzj EMDB-37954, PDB-8wzj: Human erythrocyte catalase Method: EM (single particle) / Resolution: 2.7 Å 37955 EMDB entry, No image 8wzk EMDB-37955, PDB-8wzk: Human erythrocyte catalase Method: EM (single particle) / Resolution: 2.4 Å 37956 EMDB entry, No image 8wzm EMDB-37956, PDB-8wzm: Human erythrocyte catalase with CTAB as additive during EM sample preparation Method: EM (single particle) / Resolution: 2.7 Å EMDB entry, No image EMDB-39808: E.coli. beta-galactosidase Method: EM (single particle) / Resolution: 2.8 Å EMDB entry, No image EMDB-39809: Beta-Galactosidase with N-terminus poly-histidine tag Method: EM (single particle) / Resolution: 3.1 Å
Chemicals	ChemComp-HEM: PROTOPORPHYRIN IX CONTAINING FE ChemComp-NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose
Source	homo sapiens (human) severe acute respiratory syndrome coronavirus 2 Escherichia coli (E. coli)
Keywords	OXIDOREDUCTASE / Catalase / heme / NADP / VIRAL PROTEIN / Glycoprotein / SARS-CoV-2