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Structure paper

TitleAnalysis of Global and Site-Specific Radiation Damage in Cryo-EM.
Journal, issue, pagesStructure, Vol. 26, Issue 5, Page 759-766.e4, Year 2018
Publish dateMay 1, 2018
AuthorsJohan Hattne / Dan Shi / Calina Glynn / Chih-Te Zee / Marcus Gallagher-Jones / Michael W Martynowycz / Jose A Rodriguez / Tamir Gonen /
PubMed AbstractMicro-crystal electron diffraction (MicroED) combines the efficiency of electron scattering with diffraction to allow structure determination from nano-sized crystalline samples in cryoelectron ...Micro-crystal electron diffraction (MicroED) combines the efficiency of electron scattering with diffraction to allow structure determination from nano-sized crystalline samples in cryoelectron microscopy (cryo-EM). It has been used to solve structures of a diverse set of biomolecules and materials, in some cases to sub-atomic resolution. However, little is known about the damaging effects of the electron beam on samples during such measurements. We assess global and site-specific damage from electron radiation on nanocrystals of proteinase K and of a prion hepta-peptide and find that the dynamics of electron-induced damage follow well-established trends observed in X-ray crystallography. Metal ions are perturbed, disulfide bonds are broken, and acidic side chains are decarboxylated while the diffracted intensities decay exponentially with increasing exposure. A better understanding of radiation damage in MicroED improves our assessment and processing of all types of cryo-EM data.
External linksStructure / PubMed:29706530 / PubMed Central
MethodsEM (electron crystallography)
Resolution1.01 - 3.2 Å
Structure data

EMDB-7490, PDB-6cl7:
1.71 A MicroED structure of proteinase K at 0.86 e- / A^2
Method: EM (electron crystallography) / Resolution: 1.71 Å

EMDB-7491, PDB-6cl8:
2.00 A MicroED structure of proteinase K at 2.6 e- / A^2
Method: EM (electron crystallography) / Resolution: 2.0 Å

EMDB-7492, PDB-6cl9:
2.20 A MicroED structure of proteinase K at 4.3 e- / A^2
Method: EM (electron crystallography) / Resolution: 2.2 Å

EMDB-7493, PDB-6cla:
2.80 A MicroED structure of proteinase K at 6.0 e- / A^2
Method: EM (electron crystallography) / Resolution: 2.8 Å

EMDB-7494, PDB-6clb:
3.20 A MicroED structure of proteinase K at 7.8 e- / A^2
Method: EM (electron crystallography) / Resolution: 3.2 Å

EMDB-7495, PDB-6clc:
1.01 A MicroED structure of GSNQNNF at 0.27 e- / A^2
Method: EM (electron crystallography) / Resolution: 1.01 Å

EMDB-7496, PDB-6cld:
1.01 A MicroED structure of GSNQNNF at 0.81 e- / A^2
Method: EM (electron crystallography) / Resolution: 1.01 Å

EMDB-7497, PDB-6cle:
1.01 A MicroED structure of GSNQNNF at 1.3 e- / A^2
Method: EM (electron crystallography) / Resolution: 1.01 Å

EMDB-7498, PDB-6clf:
1.15 A MicroED structure of GSNQNNF at 1.9 e- / A^2
Method: EM (electron crystallography) / Resolution: 1.15 Å

EMDB-7499, PDB-6clg:
1.35 A MicroED structure of GSNQNNF at 2.4 e- / A^2
Method: EM (electron crystallography) / Resolution: 1.35 Å

EMDB-7500, PDB-6clh:
1.37 A MicroED structure of GSNQNNF at 2.9 e- / A^2
Method: EM (electron crystallography) / Resolution: 1.37 Å

EMDB-7501, PDB-6cli:
1.01 A MicroED structure of GSNQNNF at 0.17 e- / A^2
Method: EM (electron crystallography) / Resolution: 1.01 Å

EMDB-7502, PDB-6clj:
1.01 A MicroED structure of GSNQNNF at 0.50 e- / A^2
Method: EM (electron crystallography) / Resolution: 1.01 Å

EMDB-7503, PDB-6clk:
1.01 A MicroED structure of GSNQNNF at 0.82 e- / A^2
Method: EM (electron crystallography) / Resolution: 1.01 Å

EMDB-7504, PDB-6cll:
1.02 A MicroED structure of GSNQNNF at 1.2 e- / A^2
Method: EM (electron crystallography) / Resolution: 1.02 Å

EMDB-7505, PDB-6clm:
1.01 A MicroED structure of GSNQNNF at 1.5 e- / A^2
Method: EM (electron crystallography) / Resolution: 1.01 Å

EMDB-7506, PDB-6cln:
1.15 A MicroED structure of GSNQNNF at 1.8 e- / A^2
Method: EM (electron crystallography) / Resolution: 1.15 Å

EMDB-7507, PDB-6clo:
1.15 A MicroED structure of GSNQNNF at 2.1 e- / A^2
Method: EM (electron crystallography) / Resolution: 1.15 Å

EMDB-7508, PDB-6clp:
1.16 A MicroED structure of GSNQNNF at 2.5 e- / A^2
Method: EM (electron crystallography) / Resolution: 1.16 Å

EMDB-7509, PDB-6clq:
1.21 A MicroED structure of GSNQNNF at 2.8 e- / A^2
Method: EM (electron crystallography) / Resolution: 1.21 Å

EMDB-7510, PDB-6clr:
1.31 A MicroED structure of GSNQNNF at 3.1 e- / A^2
Method: EM (electron crystallography) / Resolution: 1.31 Å

EMDB-7511, PDB-6cls:
1.46 A MicroED structure of GSNQNNF at 3.4 e- / A^2
Method: EM (electron crystallography) / Resolution: 1.46 Å

EMDB-7512, PDB-6clt:
1.45 A MicroED structure of GSNQNNF at 3.8 e- / A^2
Method: EM (electron crystallography) / Resolution: 1.45 Å

Chemicals

ChemComp-ACT:
ACETATE ION

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER

Source
  • Engyodontium album (fungus)
  • parengyodontium album (fungus)
  • synthetic construct (others)
KeywordsHYDROLASE / PROTEIN FIBRIL / Amyloid fibril / prion / zinc binding

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