|Entry||Database: EMDB / ID: EMD-0865|
|Title||MicroED structure of proteinase K at 1.50A determained using crystal lamellas prepared by focused ion beam milling|
Proteinase K / (ligand) x 2
|Function / homology|
Function and homology information
peptidase K / serine-type endopeptidase activity / metal ion binding
Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase S8, subtilisin-related / Peptidase S8, subtilisin, His-active site / Peptidase S8, subtilisin, Asp-active site / Peptidase S8, subtilisin, Ser-active site / Proteinase K-like catalytic domain / Peptidase S8/S53 domain superfamily / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily
|Biological species||Parengyodontium album (fungus) / Tritirachium album,Engyodontium album|
|Method||electron crystallography / cryo EM / Resolution: 1.5 Å|
|Authors||Zhou H / Luo Z / Li X|
|Funding support|| China, 4 items |
|Citation||Journal: J Struct Biol / Year: 2019|
Title: Using focus ion beam to prepare crystal lamella for electron diffraction.
Authors: Heng Zhou / Zhipu Luo / Xueming Li /
Abstract: Electron diffraction provides a powerful tool to solve the structures of small protein crystals. However, strong interactions between the electrons and the materials limit the application of the ...Electron diffraction provides a powerful tool to solve the structures of small protein crystals. However, strong interactions between the electrons and the materials limit the application of the electron crystallographic method on large protein crystals with micrometer or larger sizes. Here, we used the focused ion beam (FIB) equipped on the scanning electron microscope (SEM) to mill a large crystal to thin lamella. The influences of the milling on the crystal lamella were observed and investigated, including radiation damage on the crystal surface during the FIB imaging, deformation of the thin crystal lamella, and variation in the diffraction intensities under electron radiation. These observations provide important information to optimize the FIB milling, and hence is important to obtain high-quality crystal samples for routine structure determination of protein crystals using the electron cryo-microscope.
|Validation Report||PDB-ID: 6law|
SummaryFull reportAbout validation report
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_0865.map.gz / Format: CCP4 / Size: 5.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
generated in cubic-lattice coordinate
|Voxel size||X: 0.4951 Å / Y: 0.4951 Å / Z: 0.50056 Å|
|Symmetry||Space group: 96|
CCP4 map header:
-Entire proteinase K
|Entire||Name: proteinase K / Number of components: 4|
-Component #1: protein, proteinase K
|Protein||Name: proteinase K / Recombinant expression: No|
|Source||Species: Parengyodontium album (fungus)|
-Component #2: protein, Proteinase K
|Protein||Name: Proteinase K / Number of Copies: 1 / Recombinant expression: No|
|Mass||Theoretical: 28.958791 kDa|
|Source||Species: Tritirachium album,Engyodontium album|
-Component #3: ligand, SULFATE ION
|Ligand||Name: SULFATE IONSulfate / Number of Copies: 1 / Recombinant expression: No|
|Mass||Theoretical: 9.606305 MDa|
-Component #4: ligand, water
|Ligand||Name: water / Number of Copies: 230 / Recombinant expression: No|
|Mass||Theoretical: 1.801505 MDa|
|Specimen||Specimen state: 3D array / Method: cryo EM|
|Crystal parameters||Space group: P43212 / A: 69.31 Å / B: 69.31 Å / C: 104.12 Å / α: 90 %deg; / β: 90 %deg; / γ: 90 %deg;|
|Sample solution||pH: 7.5|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 0.028 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: DIFFRACTION|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN ULTRASCAN 4000 (4k x 4k)|
|Processing||Method: electron crystallography|
|3D reconstruction||Resolution: 1.5 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES|
-Atomic model buiding
|Modeling #1||Refinement protocol: flexible / Refinement space: RECIPROCAL|
-Aug 12, 2020. New: Covid-19 info
New: Covid-19 info
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info
+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. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
+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. See below links for details.
- 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.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.:Omokage search
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.
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