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- EMDB-7493: 2.80 A MicroED structure of proteinase K at 6.0 e- / A^2 -

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Basic information

Entry
Database: EMDB / ID: EMD-7493
Title2.80 A MicroED structure of proteinase K at 6.0 e- / A^2
Map data2.80 A MicroED density map of proteinase K at 6.0 e- / A^2
Sample
  • Organelle or cellular component: Proteinase K
    • Protein or peptide: Proteinase K
KeywordsHydrolase
Function / homology
Function and homology information


peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / : / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. ...Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / : / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
Biological speciesEngyodontium album (fungus) / Parengyodontium album (fungus)
Methodelectron crystallography / cryo EM / Resolution: 2.8 Å
AuthorsHattne J / Shi D
CitationJournal: 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.
History
DepositionMar 2, 2018-
Header (metadata) releaseMay 2, 2018-
Map releaseMay 16, 2018-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.19626
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.19626
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6cla
  • Surface level: 0.19626
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7493.png

Downloads & links

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Map

FileDownload / File: emd_7493.map.gz / Format: CCP4 / Size: 759.8 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation2.80 A MicroED density map of proteinase K at 6.0 e- / A^2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.9 Å/pix.
x 62 pix.
= 100.818 Å		0.94 Å/pix.
x 54 pix.
= 67.45 Å		0.94 Å/pix.
x 58 pix.
= 67.45 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 0.93681 Å / Y: 0.93681 Å / Z: 0.90016 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.19626 / Movie #1: 0.19626
Minimum - Maximum-0.20221223 - 0.57442474
Average (Standard dev.)-0.007817515 (±0.13083701)
SymmetrySpace group: 96
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-5-47-31
Dimensions545862
Spacing7272112
CellA: 67.4502 Å / B: 67.4502 Å / C: 100.8179 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.936805555555560.936805555555560.90016071428571
M x/y/z7272112
origin x/y/z0.0000.0000.000
length x/y/z67.45067.450100.818
α/β/γ90.00090.00090.000
start NX/NY/NZ-5-47-31
NX/NY/NZ545862
MAP C/R/S213
start NC/NR/NS-47-5-31
NC/NR/NS585462
D min/max/mean-0.2020.574-0.008

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Supplemental data

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Sample components

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Entire : Proteinase K

EntireName: Proteinase K
Components
  • Organelle or cellular component: Proteinase K
    • Protein or peptide: Proteinase K

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Supramolecule #1: Proteinase K

SupramoleculeName: Proteinase K / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Engyodontium album (fungus)
Molecular weightTheoretical: 28.888994 KDa

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Macromolecule #1: Proteinase K

MacromoleculeName: Proteinase K / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidase K
Source (natural)Organism: Parengyodontium album (fungus)
Molecular weightTheoretical: 28.930783 KDa
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state3D array

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Sample preparation

Concentration25 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
1.2 MN2H8SO4Ammonium sulfate
0.1 MC4H11NO3Tris
VitrificationCryogen name: ETHANE / Chamber humidity: 30 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm 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: 240 / Number diffraction images: 240 / Average exposure time: 5.1 sec. / Average electron dose: 0.0357 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 1200 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Molecular replacementSoftware - Name: MOLREP (ver. 11.4.05)
Symmetry determination software listSoftware - Name: POINTLESS (ver. 1.11.3)
Merging software listSoftware - Name: AIMLESS (ver. 0.5.32)
Crystallography statisticsNumber intensities measured: 30596 / Number structure factors: 5423 / Fourier space coverage: 88.4 / R sym: 0.536 / R merge: 0.536 / Overall phase error: 62.59 / Overall phase residual: 62.59 / Phase error rejection criteria: 0 / High resolution: 2.8 Å / Shell - Shell ID: 1 / Shell - High resolution: 2.8 Å / Shell - Low resolution: 2.87 Å / Shell - Number structure factors: 374 / Shell - Phase residual: 71.28 / Shell - Fourier space coverage: 88.21 / Shell - Multiplicity: 5.8

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Atomic model buiding 1

Initial modelPDB ID:

5i9s


Chain - Chain ID: A / Chain - Residue range: 1-279 / Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsElectron scattering factors
RefinementSpace: RECIPROCAL / Protocol: OTHER / Overall B value: 29.658
Output model

PDB-6cla:
2.80 A MicroED structure of proteinase K at 6.0 e- / A^2

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