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TitleAddressing compressive deformation of proteins embedded in crystalline ice.
Journal, issue, pagesStructure, Vol. 31, Issue 2, Page 213-220.e3, Year 2023
Publish dateFeb 2, 2023
AuthorsHuigang Shi / Chunling Wu / Xinzheng Zhang /
PubMed AbstractFor 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 linksStructure / PubMed:36586403
MethodsEM (single particle)
Resolution1.76 - 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)
  • cattle (cattle)
  • oryctolagus cuniculus (rabbit)
  • rabbit (rabbit)
  • homo sapiens (human)
  • coxsackievirus a10
  • enterovirus a71
KeywordsVIRUS / 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

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