|Entry||Database: EMDB / ID: EMD-7490|
|Title||1.71 A MicroED structure of proteinase K at 0.86 e- / A^2|
|Function / homology|
Function and homology information
peptidase K / serine-type endopeptidase activity / metal ion binding
Proteinase K-like catalytic domain / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase S8, subtilisin-related / Peptidase S8, subtilisin, His-active site / Peptidase S8, subtilisin, Asp-active site / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase family, serine active site. ...Proteinase K-like catalytic domain / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase S8, subtilisin-related / Peptidase S8, subtilisin, His-active site / Peptidase S8, subtilisin, Asp-active site / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8/S53 domain superfamily / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Subtilase family / Peptidase inhibitor I9 / Serine proteases, subtilase family, aspartic acid active site.
|Biological species||Engyodontium album (fungus) / Engyodontium album, Tritirachium album|
|Method||electron crystallography / cryo EM / Resolution: 1.71 Å|
|Authors||Hattne J / Shi D / Glynn C / Zee C-T / Gallagher-Jones M / Martynowycz MW / Rodriguez JA / Gonen T|
|Citation||Journal: Structure / Year: 2018|
Title: Analysis of Global and Site-Specific Radiation Damage in Cryo-EM.
Authors: Johan Hattne / Dan Shi / Calina Glynn / Chih-Te Zee / Marcus Gallagher-Jones / Michael W Martynowycz / Jose A Rodriguez / Tamir Gonen /
Abstract: Micro-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.
|Validation Report||PDB-ID: 6cl7|
SummaryFull reportAbout validation report
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_7490.map.gz / Format: CCP4 / Size: 3.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
generated in cubic-lattice coordinate
|Voxel size||X: 0.55842 Å / Y: 0.55842 Å / Z: 0.57229 Å|
|Symmetry||Space group: 96|
CCP4 map header:
-Entire Proteinase K
|Entire||Name: Proteinase K / Number of components: 2|
-Component #1: cellular-component, Proteinase K
|Cellular-component||Name: Proteinase K / Recombinant expression: No|
|Mass||Theoretical: 28.888994 kDa|
|Source||Species: Engyodontium album (fungus)|
-Component #2: protein, Proteinase K
|Protein||Name: Proteinase K / Number of Copies: 1 / Recombinant expression: No|
|Mass||Theoretical: 28.930783 kDa|
|Source||Species: Engyodontium album, Tritirachium album|
|Specimen||Specimen state: 3D array / Method: cryo EM|
|Crystal parameters||Space group: P43212 / A: 67.0104 Å / B: 67.0104 Å / C: 100.722 Å / α: 90 %deg; / β: 90 %deg; / γ: 90 %deg;|
|Sample solution||Specimen conc.: 25 mg/mL / pH: 8|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 30 %|
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 0.0357 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: DIFFRACTION|
|Specimen Holder||Model: OTHER|
|Camera||Detector: TVIPS TEMCAM-F416 (4k x 4k)|
|Image acquisition||Number of digital images: 289 / Sampling size: 31.2 µm|
|Processing||Method: electron crystallography|
|3D reconstruction||Resolution: 1.71 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES|
-Atomic model buiding
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