[English] 日本語
Yorodumi
- EMDB-70378: MicroED structure of proteinase K without energy filtering -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-70378
TitleMicroED structure of proteinase K without energy filtering
Map data
Sample
  • Complex: Proteinase K
    • Protein or peptide: Proteinase K
  • Ligand: CALCIUM ION
  • Ligand: NITRATE ION
  • Ligand: water
Keywordsserine protease / hydrolase
Function / homology
Function and homology information


peptidase K / serine-type endopeptidase activity / proteolysis / extracellular region / 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 speciesParengyodontium album (fungus)
Methodelectron crystallography / cryo EM / Resolution: 1.3 Å
AuthorsClabbers MTB / Gonen T / Martynoqycz MW
Funding support United States, 3 items
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, 2025-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_70378.png

Downloads & links

-
Map

FileDownload / File: emd_70378.map.gz / Format: CCP4 / Size: 25.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.31 Å/pix.
x 185 pix.
= 57.924 Å		0.31 Å/pix.
x 192 pix.
= 60.115 Å		0.31 Å/pix.
x 190 pix.
= 59.489 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.3131 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.47
Minimum - Maximum-2.1691077 - 13.995139
Average (Standard dev.)-0.0044670943 (±0.98200655)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin-42-102-159
Dimensions192190185
Spacing185192190
CellA: 57.9235 Å / B: 60.115204 Å / C: 59.489002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Proteinase K

EntireName: Proteinase K
Components
  • Complex: Proteinase K
    • Protein or peptide: Proteinase K
  • Ligand: CALCIUM ION
  • Ligand: NITRATE ION
  • Ligand: water

-
Supramolecule #1: Proteinase K

SupramoleculeName: Proteinase K / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Serine protease
Source (natural)Organism: Parengyodontium album (fungus)
Molecular weightTheoretical: 28.9 KDa

-
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: 28.958791 KDa
Recombinant expressionOrganism: Parengyodontium album (fungus)
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 LDIFGPGTDI LSTWIGGSTR SISGTSMATP HVAGLAAYLM TL GKTTAAS ACRYIADTAN KGDLSNIPFG TVNLLAYNNY QA

UniProtKB: Proteinase K

-
Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Macromolecule #3: NITRATE ION

MacromoleculeName: NITRATE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: NO3
Molecular weightTheoretical: 62.005 Da
Chemical component information

ChemComp-NO3:
NITRATE ION

-
Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 375 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state3D array

-
Sample preparation

Concentration40 mg/mL
BufferpH: 6.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 10 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Details: Negative 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: LEICA PLUNGER
DetailsMicrocrystals

-
Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 77.0 K / Max: 90.0 K
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 1 / Number diffraction images: 420 / Average exposure time: 1.0 sec. / Average electron dose: 0.002 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 0.0 µm / Nominal defocus min: 0.0 µm / Camera length: 1402 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.3 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Software - Name: PHENIX (ver. 1.21.1)
CTF correctionType: NONE
Molecular replacementSoftware - Name: PHASER (ver. 2.8.3)
Symmetry determination software listSoftware - Name: XDS (ver. BUILT=20230630)
Merging software listSoftware - Name: XSCALE (ver. BUILT=20230630)
Crystallography statisticsNumber intensities measured: 2811895 / Number structure factors: 98228 / Fourier space coverage: 97.5 / R merge: 28.4 / Overall phase residual: 0 / Phase error rejection criteria: None / High resolution: 1.09 Å / Shell - Shell ID: 1 / Shell - High resolution: 1.09 Å / Shell - Low resolution: 56.82 Å / Shell - Number structure factors: 98228 / Shell - Phase residual: 16.04 / Shell - Fourier space coverage: 97.5 / Shell - Multiplicity: 28.5

-
Atomic model buiding 1

Initial modelPDB ID:

9dho


Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: Molecular replacement
RefinementSpace: RECIPROCAL / Protocol: OTHER / Overall B value: 11.57 / Target criteria: Maximum likelihood
Output model

PDB-9odv:
MicroED structure of proteinase K without energy filtering

+
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