+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-7490 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | 1.71 A MicroED structure of proteinase K at 0.86 e- / A^2 | |||||||||
![]() | 1.71 A MicroED density map of proteinase K at 0.86 e- / A^2 | |||||||||
![]() |
| |||||||||
![]() | Hydrolase | |||||||||
Function / homology | ![]() peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | electron crystallography / cryo EM / Resolution: 1.71 Å | |||||||||
![]() | Hattne J / Shi D | |||||||||
![]() | ![]() 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. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 2.9 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 13.7 KB 13.7 KB | Display Display | ![]() |
Images | ![]() | 200.7 KB | ||
Filedesc metadata | ![]() | 5.3 KB | ||
Filedesc structureFactors | ![]() | 1.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 618 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 617.6 KB | Display | |
Data in XML | ![]() | 4.2 KB | Display | |
Data in CIF | ![]() | 4.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6cl7MC ![]() 7491C ![]() 7492C ![]() 7493C ![]() 7494C ![]() 7495C ![]() 7496C ![]() 7497C ![]() 7498C ![]() 7499C ![]() 7500C ![]() 7501C ![]() 7502C ![]() 7503C ![]() 7504C ![]() 7505C ![]() 7506C ![]() 7507C ![]() 7508C ![]() 7509C ![]() 7510C ![]() 7511C ![]() 7512C ![]() 6cl8C ![]() 6cl9C ![]() 6claC ![]() 6clbC ![]() 6clcC ![]() 6cldC ![]() 6cleC ![]() 6clfC ![]() 6clgC ![]() 6clhC ![]() 6cliC ![]() 6cljC ![]() 6clkC ![]() 6cllC ![]() 6clmC ![]() 6clnC ![]() 6cloC ![]() 6clpC ![]() 6clqC ![]() 6clrC ![]() 6clsC ![]() 6cltC C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | 1.71 A MicroED density map of proteinase K at 0.86 e- / A^2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 0.55842 Å / Y: 0.55842 Å / Z: 0.57229 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 96 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : Proteinase K
Entire | Name: Proteinase K |
---|---|
Components |
|
-Supramolecule #1: Proteinase K
Supramolecule | Name: Proteinase K / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 28.888994 KDa |
-Macromolecule #1: Proteinase K
Macromolecule | Name: Proteinase K / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidase K |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 28.930783 KDa |
Sequence | String: AAQTNAPWGL ARISSTSPGT STYYYDESAG QGSCVYVIDT GIEASHPEFE GRAQMVKTYY YSSRDGNGHG THCAGTVGSR TYGVAKKTQ LFGVKVLDDN GSGQYSTIIA GMDFVASDKN NRNCPKGVVA SLSLGGGYSS SVNSAAARLQ SSGVMVAVAA G NNNADARN ...String: AAQTNAPWGL ARISSTSPGT STYYYDESAG QGSCVYVIDT GIEASHPEFE GRAQMVKTYY YSSRDGNGHG THCAGTVGSR TYGVAKKTQ LFGVKVLDDN GSGQYSTIIA GMDFVASDKN NRNCPKGVVA SLSLGGGYSS SVNSAAARLQ SSGVMVAVAA G NNNADARN YSPASEPSVC TVGASDRYDR RSSFSNYGSV LDIFGPGTSI LSTWIGGSTR SISGTSMATP HVAGLAAYLM TL GKTTAAS ACRYIADTAN KGDLSNIPFG TVNLLAYNNY QA UniProtKB: Proteinase K |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | electron crystallography |
Aggregation state | 3D array |
-
Sample preparation
Concentration | 25 mg/mL | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8 Component:
| |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 30 % / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Number grids imaged: 1 / Number real images: 289 / Number diffraction images: 289 / Average exposure time: 5.1 sec. / Average electron dose: 0.0357 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 1200 mm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
+
Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Residue range: 1-279 / Chain - Source name: PDB / Chain - Initial model type: experimental model |
---|---|
Details | Electron scattering factors |
Refinement | Space: RECIPROCAL / Protocol: OTHER / Overall B value: 6.613 |
Output model | ![]() PDB-6cl7: |