-Browse 3DEM data
-Recently released data
-Sep 18, 2019 (EMDB: 47 / PDB: 34)
+Sep 11, 2019 (EMDB: 52 / PDB: 38)
+Sep 4, 2019 (EMDB: 35 / PDB: 30)
Other latests: New EMDB meta data, Updated EMDBs, Updated PDBsQ: When the data are updated?
-Recent 3DEM papers
-Mitoribosomal small subunit biogenesis in trypanosomes involves an extensive assembly machinery.
Science, Vol. 365, Issue 6458, Page 1144-1149, Year 2019
Martin Saurer / David J F Ramrath / Moritz Niemann / Salvatore Calderaro / Céline Prange / Simone Mattei / Alain Scaiola / Alexander Leitner / Philipp Bieri / Elke K Horn / Marc Leibundgut / Daniel Boehringer / André Schneider / Nenad Ban
Methods: EM (single particle)
-Electron cryo-microscopy of Bacteriophage PR772 reveals the elusive vertex complex and the capsid architecture.
+Structural insights into TRPM8 inhibition and desensitization.
+A unified mechanism for intron and exon definition and back-splicing.
Nature, Year 2019
Xueni Li / Shiheng Liu / Lingdi Zhang / Aaron Issaian / Ryan C Hill / Sara Espinosa / Shasha Shi / Yanxiang Cui / Kalli Kappel / Rhiju Das / Kirk C Hansen / Z Hong Zhou / Rui Zhao
Methods: EM (single particle)
+DNA-Packing Portal and Capsid-Associated Tegument Complexes in the Tumor Herpesvirus KSHV.
-About EM Navigator
-Jul 5, 2019. Downlodablable text data
Downlodablable text data
- Some data of EM Navigator services can be downloaded as text file. Software such as Excel can load the data files.
Page Data Format EMN Search search result CSV, TSV, or JSON EMN statistics data table CSV or TSV
Related info.: EMN Search / EMN Statistics
-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
+Feb 20, 2018. PDBj/BINDS workshop in Osaka University
PDBj/BINDS workshop in Osaka University
+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.
3D electron microscopy data browser
- Browser for 3D electron microscopy (3D-EM) data of biological molecules and assemblies.
Related info.: EMDB / PDB / PDBj / Q: What is the data source of EM Navigator? / EMN Search / EMN Papers / EMN Gallery / EMN Statistics / Changes in new EM Navigator and Yorodumi