[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

TitleThe box C/D sRNP dimeric architecture is conserved across domain Archaea.
Journal, issue, pagesRNA, Vol. 18, Issue 8, Page 1527-1540, Year 2012
Publish dateJul 17, 2012
AuthorsKathleen R Bower-Phipps / David W Taylor / Hong-Wei Wang / Susan J Baserga
External linksPubMed:22753779 / Publisher's page
MethodsEM (single particle)
Resolution25 - 26 A
Structure data

EMDB-5419:
Sulfolobus solfataricus methylation-guide sRNP

EMDB-5420:
Pyrococcus abyssi methylation-guide sRNP

EMDB-5421:
Archaeoglobus fulgidus methylation-guide sRNP

SourceSulfolobus solfataricus / archaea / thermophilic / スルホロブス・ソルファタリカス
Pyrococcus abyssi / archaea / thermophilic
Archaeoglobus fulgidus / archaea / thermophilic / アーキオグロブス・フルギダス
Keywordsarchaea / box C/D sRNP / single particle EM / rRNA modification / RNA-protein complex / non-coding RNA / Archaea / Archaeal Proteins / Base Sequence / Methylation / Molecular Sequence Data / Mutagenesis / Protein Binding / Protein Conformation / Protein Multimerization / RNA, Archaeal / RNA, Small Nucleolar / Ribonucleoproteins, Small Nucleolar

+
About Yorodumi Papers

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
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.

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

+
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

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more

-
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