[English] 日本語
Yorodumi
- PDB-9odw: MicroED structure of proteinase K with energy filtering -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9odw
TitleMicroED structure of proteinase K with energy filtering
ComponentsProteinase K
KeywordsHYDROLASE / serine protease
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
NITRATE ION / Proteinase K
Similarity search - Component
Biological speciesParengyodontium album (fungus)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 1.3 Å
AuthorsClabbers, M.T.B. / Gonen, T.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM136508 United States
Department of Defense (DOD, United States)HDTRA1-21-1-0004 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Struct Dyn / Year: 2025
Title: Recovering high-resolution information using energy filtering in MicroED.
Authors: Max T B Clabbers / Tamir Gonen
Abstract: Inelastic scattering poses a significant challenge in electron crystallography by elevating background noise and broadening Bragg peaks, thereby reducing the overall signal-to-noise ratio. This is ...Inelastic scattering poses a significant challenge in electron crystallography by elevating background noise and broadening Bragg peaks, thereby reducing the overall signal-to-noise ratio. This is particularly detrimental to data quality in structural biology, as the diffraction signal is relatively weak. These effects are aggravated even further by the decay of the diffracted intensities as a result of accumulated radiation damage, and rapidly fading high-resolution information can disappear beneath the noise. Loss of high-resolution reflections can partly be mitigated using energy filtering, which removes inelastically scattered electrons and improves data quality and resolution. Here, we systematically compared unfiltered and energy-filtered microcrystal electron diffraction data from proteinase K crystals, first collecting an unfiltered dataset followed directly by a second sweep using the same settings but with the energy filter inserted. Our results show that energy filtering consistently reduces noise, sharpens Bragg peaks, and extends high-resolution information, even though the absorbed dose was doubled for the second pass. Importantly, our results demonstrate that high-resolution information can be recovered by inserting the energy filter slit. Energy-filtered datasets showed improved intensity statistics and better internal consistency, highlighting the effectiveness of energy filtering for improving data quality. These findings underscore its potential to overcome limitations in macromolecular electron crystallography, enabling higher-resolution structures with greater reliability.
History
DepositionApr 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1014
Polymers28,9591
Non-polymers1423
Water5,567309
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.640, 67.640, 106.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-607-

HOH

21A-777-

HOH

-
Components

#1: Protein Proteinase K / Endopeptidase K / Tritirachium alkaline proteinase


Mass: 28958.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parengyodontium album (fungus) / Gene: PROK / Production host: Parengyodontium album (fungus) / References: UniProt: P06873, peptidase K
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

-
Sample preparation

ComponentName: Proteinase K / Type: COMPLEX / Details: Serine protease / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.0289 MDa / Experimental value: NO
Source (natural)Organism: Parengyodontium album (fungus)
Source (recombinant)Organism: Parengyodontium album (fungus)
Buffer solutionpH: 6.5
SpecimenConc.: 40 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Microcrystals
Specimen supportDetails: Negative 15 mA / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA PLUNGER / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

-
Data collection

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 0 nm / Nominal defocus min: 0 nm / C2 aperture diameter: 50 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 90 K / Temperature (min): 77 K
Image recordingAverage exposure time: 1 sec. / Electron dose: 0.002 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of diffraction images: 420 / Num. of grids imaged: 1 / Num. of real images: 1
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096
EM diffractionCamera length: 1402 mm
EM diffraction shellResolution: 1.09→56.82 Å / Fourier space coverage: 97.5 % / Multiplicity: 28.5 / Num. of structure factors: 98228 / Phase residual: 16.04 °
EM diffraction statsFourier space coverage: 97.5 % / High resolution: 1.09 Å / Num. of intensities measured: 2811895 / Num. of structure factors: 98228 / Phase error rejection criteria: None / Rmerge: 28.4
ReflectionBiso Wilson estimate: 10.26 Å2

-
Processing

EM software
IDNameVersionCategory
1SerialEM4.2.0image acquisition
6Coot0.9.8.93model fitting
8PHENIX1.21.1model refinement
9PHASER2.8.3molecular replacement
11XDSBUILT=20230630symmetry determination
12XSCALEBUILT=20230630crystallography merging
13PHENIX1.21.13D reconstruction
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 67.64 Å / B: 67.64 Å / C: 106.67 Å / Space group name: P43322 / Space group num: 96
CTF correctionType: NONE
3D reconstructionResolution: 1.3 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingB value: 12.61 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: Maximum likelihood
Atomic model buildingPDB-ID: 9dho

9dho


Accession code: 9dho / Details: Molecular replacement / Source name: PDB / Type: experimental model
RefinementResolution: 1.3→43.64 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.4664
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2279 2868 4.91 %
Rwork0.1888 55574 -
obs0.1908 58442 95.01 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.61 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.00912277
ELECTRON CRYSTALLOGRAPHYf_angle_d1.01813128
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.0848338
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.0085429
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d12.9065806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.39151460.33032697ELECTRON CRYSTALLOGRAPHY94.23
1.32-1.350.35711370.31752714ELECTRON CRYSTALLOGRAPHY93.84
1.35-1.370.36231380.30642703ELECTRON CRYSTALLOGRAPHY94.17
1.37-1.40.34081300.29972724ELECTRON CRYSTALLOGRAPHY94.41
1.4-1.430.32451420.28012733ELECTRON CRYSTALLOGRAPHY94.92
1.43-1.460.32821480.26232731ELECTRON CRYSTALLOGRAPHY94.77
1.46-1.50.24791210.25322762ELECTRON CRYSTALLOGRAPHY94.9
1.5-1.540.2921490.23842760ELECTRON CRYSTALLOGRAPHY95.07
1.54-1.590.31541390.23182714ELECTRON CRYSTALLOGRAPHY95.1
1.59-1.640.28851360.22642778ELECTRON CRYSTALLOGRAPHY95.14
1.64-1.70.25171430.21232779ELECTRON CRYSTALLOGRAPHY95.27
1.7-1.760.2561440.20232760ELECTRON CRYSTALLOGRAPHY95.43
1.76-1.840.25691460.20062769ELECTRON CRYSTALLOGRAPHY95.17
1.84-1.940.25651600.18482773ELECTRON CRYSTALLOGRAPHY95.2
1.94-2.060.19121410.16882790ELECTRON CRYSTALLOGRAPHY95.6
2.06-2.220.23121400.16682812ELECTRON CRYSTALLOGRAPHY95.63
2.22-2.450.22411550.17492823ELECTRON CRYSTALLOGRAPHY95.72
2.45-2.80.18511400.1692863ELECTRON CRYSTALLOGRAPHY95.58
2.8-3.530.16131550.1462872ELECTRON CRYSTALLOGRAPHY95.52
3.53-43.640.16461580.13623017ELECTRON CRYSTALLOGRAPHY94.63

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more