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	Addressing compressive deformation of proteins embedded in crystalline ice.
Journal, issue, pages	Structure, Vol. 31, Issue 2, Page 213-220.e3, Year 2023
Publish date	Feb 2, 2023
Authors	Huigang Shi / Chunling Wu / Xinzheng Zhang /
PubMed Abstract	For cryoelectron microscopy (cryo-EM), high cooling rates have been required for preparation of protein samples to vitrify the surrounding water and avoid formation of damaging crystalline ice. ...For cryoelectron microscopy (cryo-EM), high cooling rates have been required for preparation of protein samples to vitrify the surrounding water and avoid formation of damaging crystalline ice. Whether and how crystalline ice affects single-particle cryo-EM is still unclear. Here, single-particle cryo-EM was used to analyze three-dimensional structures of various proteins and viruses embedded in crystalline ice formed at various cooling rates. Low cooling rates led to shrinkage deformation and density distortions on samples having loose structures. Higher cooling rates reduced deformations. Deformation-free proteins in crystalline ice were obtained by modifying the freezing conditions, and reconstructions from these samples revealed a marked improvement over vitreous ice. This procedure also increased the efficiency of cryo-EM structure determinations and was essential for high-resolution reconstructions.
External links	Structure / PubMed:36586403
Methods	EM (single particle)
Resolution	1.76 - 3.2 Å
Structure data	28627 8bqn EMDB-28627: Cryo-EM structure of Coxsackievirus A10 (empty) embedded in crystalline ice PDB-8bqn: Structure of empty Coxsackievirus A10 embedded in crystalline ice frozen at -140 degree Method: EM (single particle) / Resolution: 3.1 Å 28638 8f7y EMDB-28638: Cryo-EM structure of Coxsackievirus A10 embedded in crystalline ice PDB-8f7y: Structure of Coxsackievirus A10 frozen at -183 degree embedded in crystalline ice Method: EM (single particle) / Resolution: 2.8 Å 28639 8ew0 EMDB-28639, PDB-8ew0: Cryo-EM structure of glutamate dehydrogenase frozen at various temperature Method: EM (single particle) / Resolution: 2.7 Å 28640 8ew2 EMDB-28640, PDB-8ew2: Cryo-EM structure of Aldolase embedded in crystalline ice Method: EM (single particle) / Resolution: 3.1 Å 32695 8f49 EMDB-32695: High resolution of apo-ferritin embedded in crystalline ice PDB-8f49: 1.8 angstrom structure of apoferritin embedded in crystalline ice Method: EM (single particle) / Resolution: 1.76 Å 32703 8hhs EMDB-32703: apo-ferritin embedded in crystalline ice frozen at -183 degree PDB-8hhs: Structure of human apoferritin embedded in crystalline ice Method: EM (single particle) / Resolution: 2.4 Å 32709 8hi2 EMDB-32709: EV71 VLP maps embedded in crystalline ice PDB-8hi2: Structure of EV71 VLP frozen at -183 degree embedded in crystalline ice Method: EM (single particle) / Resolution: 3.2 Å
Source	bos taurus (cattle) oryctolagus cuniculus (rabbit) homo sapiens (human) coxsackievirus a10 enterovirus a71
Keywords	VIRUS / Coxsackievirus A10 / empty Coxsackievirus A10 / crystalline ice / LYASE / glutamate dehydrogenase / GDH / Aldolase / METAL BINDING PROTEIN / ferritin / crystal ice / crystal-ice / apo-ferritin / human apo-ferritin / human ferritin / Coxsackievirus