[English] 日本語
Yorodumi
- PDB-8e53: MicroED structure of proteinase K recorded on K3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8.0E+53
TitleMicroED structure of proteinase K recorded on K3
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 / Peptidase S8/S53 domain / Subtilase family
Similarity search - Domain/homology
Biological speciesParengyodontium album (fungus)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 1.7 Å
AuthorsClabbers, M.T.B. / Martynowycz, M.W. / Hattne, J. / Nannenga, B.L. / Gonen, T.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM136508 United States
CitationJournal: J Struct Biol / Year: 2022
Title: Electron-counting MicroED data with the K2 and K3 direct electron detectors.
Authors: Max T B Clabbers / Michael W Martynowycz / Johan Hattne / Brent L Nannenga / Tamir Gonen /
Abstract: Microcrystal electron diffraction (MicroED) uses electron cryo-microscopy (cryo-EM) to collect diffraction data from small crystals during continuous rotation of the sample. As a result of advances ...Microcrystal electron diffraction (MicroED) uses electron cryo-microscopy (cryo-EM) to collect diffraction data from small crystals during continuous rotation of the sample. As a result of advances in hardware as well as methods development, the data quality has continuously improved over the past decade, to the point where even macromolecular structures can be determined ab initio. Detectors suitable for electron diffraction should ideally have fast readout to record data in movie mode, and high sensitivity at low exposure rates to accurately report the intensities. Direct electron detectors are commonly used in cryo-EM imaging for their sensitivity and speed, but despite their availability are generally not used in diffraction. Primary concerns with diffraction experiments are the dynamic range and coincidence loss, which will corrupt the measurement if the flux exceeds the count rate of the detector. Here, we describe instrument setup and low-exposure MicroED data collection in electron-counting mode using K2 and K3 direct electron detectors and show that the integrated intensities can be effectively used to solve structures of two macromolecules between 1.2 Å and 2.8 Å resolution. Even though a beam stop was not used with the K3 studies we did not observe damage to the camera. As these cameras are already available in many cryo-EM facilities, this provides opportunities for users who do not have access to dedicated facilities for MicroED.
History
DepositionAug 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0393
Polymers28,9591
Non-polymers802
Water4,756264
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.010, 67.010, 106.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11AAA-585-

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
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 supportGrid 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Cs: 2.7 mm / 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: 0.5 sec. / Electron dose: 0.01 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of diffraction images: 840 / Num. of grids imaged: 1 / Num. of real images: 1
Image scansSampling size: 5 µm / Width: 5760 / Height: 4092
EM diffractionCamera length: 745 mm
EM diffraction shellResolution: 2.7→3.4 Å / Fourier space coverage: 83 % / Multiplicity: 6 / Num. of structure factors: 2499 / Phase residual: 33 °
EM diffraction statsFourier space coverage: 83 % / High resolution: 2.7 Å / Num. of intensities measured: 30326 / Num. of structure factors: 5453 / Phase error: 28 ° / Phase error rejection criteria: None / Rmerge: 64 / Rsym: 30

-
Processing

SoftwareName: REFMAC / Version: 5.8.0267 / Classification: refinement / Contact author: Garib N. Murshudov / Contact author email: garib[at]mrc-lmb.cam.ac.uk / Date: 2020-24-08
Description: (un)restrained refinement or idealisation of macromolecular structures
EM software
IDNameCategory
11AIMLESScrystallography merging
12REFMAC3D reconstruction
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 67.01 Å / B: 67.01 Å / C: 106.56 Å / Space group name: P43212 / Space group num: 96
CTF correctionType: NONE
3D reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingB value: 15.89 / Protocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: Maximum liklihood
RefinementResolution: 1.7→43.333 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.919 / SU B: 9.248 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.132
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2542 1286 4.779 %
Rwork0.1757 25625 -
all0.179 --
obs-26911 98.14 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.889 Å2
Baniso -1Baniso -2Baniso -3
1-0.422 Å20 Å2-0 Å2
2--0.422 Å2-0 Å2
3----0.844 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON CRYSTALLOGRAPHYr_bond_refined_d0.0120.0132072
ELECTRON CRYSTALLOGRAPHYr_bond_other_d00.0141854
ELECTRON CRYSTALLOGRAPHYr_angle_refined_deg1.431.6392817
ELECTRON CRYSTALLOGRAPHYr_angle_other_deg1.6221.5784260
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_1_deg6.5295278
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_2_deg35.97121.97996
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_3_deg13.3415299
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_4_deg20.0341512
ELECTRON CRYSTALLOGRAPHYr_chiral_restr0.0650.2279
ELECTRON CRYSTALLOGRAPHYr_gen_planes_refined0.0070.022457
ELECTRON CRYSTALLOGRAPHYr_gen_planes_other0.0010.02495
ELECTRON CRYSTALLOGRAPHYr_nbd_refined0.2090.2559
ELECTRON CRYSTALLOGRAPHYr_symmetry_nbd_other0.1920.22114
ELECTRON CRYSTALLOGRAPHYr_nbtor_refined0.1790.21119
ELECTRON CRYSTALLOGRAPHYr_symmetry_nbtor_other0.0830.21057
ELECTRON CRYSTALLOGRAPHYr_xyhbond_nbd_refined0.2510.2294
ELECTRON CRYSTALLOGRAPHYr_symmetry_xyhbond_nbd_other0.1430.22
ELECTRON CRYSTALLOGRAPHYr_metal_ion_refined0.1390.23
ELECTRON CRYSTALLOGRAPHYr_symmetry_nbd_refined0.1670.214
ELECTRON CRYSTALLOGRAPHYr_nbd_other0.2060.252
ELECTRON CRYSTALLOGRAPHYr_symmetry_xyhbond_nbd_refined0.2950.217
ELECTRON CRYSTALLOGRAPHYr_mcbond_it2.1231.4731115
ELECTRON CRYSTALLOGRAPHYr_mcbond_other2.1171.471114
ELECTRON CRYSTALLOGRAPHYr_mcangle_it2.6672.2161392
ELECTRON CRYSTALLOGRAPHYr_mcangle_other2.672.2191393
ELECTRON CRYSTALLOGRAPHYr_scbond_it3.0671.82957
ELECTRON CRYSTALLOGRAPHYr_scbond_other3.0671.823958
ELECTRON CRYSTALLOGRAPHYr_scangle_it3.5142.6041425
ELECTRON CRYSTALLOGRAPHYr_scangle_other3.5142.6081426
ELECTRON CRYSTALLOGRAPHYr_lrange_it4.41530.13410325
ELECTRON CRYSTALLOGRAPHYr_lrange_other3.90529.65510063
ELECTRON CRYSTALLOGRAPHYr_rigid_bond_restr2.09633926
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.411030.3731601ELECTRON CRYSTALLOGRAPHY86.3222
1.744-1.7920.374920.3321746ELECTRON CRYSTALLOGRAPHY94.938
1.792-1.8440.37800.3021746ELECTRON CRYSTALLOGRAPHY96.87
1.844-1.9010.319760.2621705ELECTRON CRYSTALLOGRAPHY96.8988
1.901-1.9630.314820.2131694ELECTRON CRYSTALLOGRAPHY100
1.963-2.0320.279750.1871658ELECTRON CRYSTALLOGRAPHY100
2.032-2.1090.292910.1611565ELECTRON CRYSTALLOGRAPHY100
2.109-2.1940.24900.1441514ELECTRON CRYSTALLOGRAPHY100
2.194-2.2920.304630.1621480ELECTRON CRYSTALLOGRAPHY100
2.292-2.4040.253660.171418ELECTRON CRYSTALLOGRAPHY100
2.404-2.5330.252760.1651329ELECTRON CRYSTALLOGRAPHY100
2.533-2.6870.194580.1351302ELECTRON CRYSTALLOGRAPHY100
2.687-2.8720.256660.1421195ELECTRON CRYSTALLOGRAPHY100
2.872-3.1010.286490.1491132ELECTRON CRYSTALLOGRAPHY100
3.101-3.3960.23520.1351059ELECTRON CRYSTALLOGRAPHY100
3.396-3.7950.165430.121955ELECTRON CRYSTALLOGRAPHY100
3.795-4.3790.168470.117844ELECTRON CRYSTALLOGRAPHY99.8879
4.379-5.3550.181380.116735ELECTRON CRYSTALLOGRAPHY100
5.355-7.540.229200.162602ELECTRON CRYSTALLOGRAPHY100
7.54-43.30.192190.27345ELECTRON CRYSTALLOGRAPHY95.0392

+
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