[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleProgramming Conventional Electron Microscopes for Solving Ultrahigh-Resolution Structures of Small and Macro-Molecules.
Journal, issue, pagesAnal Chem, Vol. 91, Issue 17, Page 10996-11003, Year 2019
Publish dateSep 3, 2019
AuthorsHeng Zhou / Feng Luo / Zhipu Luo / Dan Li / Cong Liu / Xueming Li /
PubMed AbstractMicrocrystal electron diffraction (MicroED) is becoming a powerful tool in determining the crystal structures of biological macromolecules and small organic compounds. However, wide applications of ...Microcrystal electron diffraction (MicroED) is becoming a powerful tool in determining the crystal structures of biological macromolecules and small organic compounds. However, wide applications of this technique are still limited by the special requirement for radiation-tolerated movie-mode camera and the lack of automated data collection methods. Herein, we develop a stage-camera synchronization scheme to minimize the hardware requirements and enable the use of the conventional electron cryo-microscope with a single-frame CCD camera, which ensures not only the acquisition of ultrahigh-resolution diffraction data but also low cost in practice. This method renders the structure determination of both peptide and small organic compounds at ultrahigh resolution up to ∼0.60 Å with unambiguous assignment of nearly all hydrogen atoms. The present work provides a widely applicable solution for routine structure determination of MicroED and demonstrates the capability of the low-end 120 kV microscope with a CCD camera in solving ultrahigh resolution structures of both organic compounds and biological macromolecules.
External linksAnal Chem / PubMed:31334636
MethodsEM (electron crystallography)
Resolution0.6 - 0.67 Å
Structure data

EMDB-0696, PDB-6kj1:
200kV MicroED structure of FUS (37-42) SYSGYS solved from merged datasets at 0.65 A
Method: EM (electron crystallography) / Resolution: 0.65 Å

EMDB-0697, PDB-6kj2:
200kV MicroED structure of FUS (37-42) SYSGYS solved from single crystal at 0.67 A
Method: EM (electron crystallography) / Resolution: 0.67 Å

EMDB-0698, PDB-6kj3:
120kV MicroED structure of FUS (37-42) SYSGYS solved from merged datasets at 0.60 A
Method: EM (electron crystallography) / Resolution: 0.6 Å

EMDB-0699, PDB-6kj4:
120kV MicroED structure of FUS (37-42) SYSGYS solved from single crystal at 0.65 A
Method: EM (electron crystallography) / Resolution: 0.65 Å

Chemicals

ChemComp-HOH:
WATER / Water

Source
  • homo sapiens (human)
KeywordsRNA BINDING PROTEIN / FUS / MicroED / Ultrahigh resolution

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more