-Browse 3DEM data
-Recently released data
-Nov 14, 2018 (EMDB: 31, PDB:12)
+Nov 7, 2018 (EMDB: 22, PDB:20)
+Oct 31, 2018 (EMDB: 13, PDB:5)Q: When the data are updated?
-Recent 3DEM papers
-Visualization of clustered protocadherin neuronal self-recognition complexes
Nature, Vol. tbd
Brasch J / Goodman KM / Noble AJ / Rapp M / Mannepalli S / Bahna F / Dandey VP / Bepler T / Berger B / Maniatis T / Potter CS / Carragher B / Honig B / Shapiro L
Methods: EM (subtomogram averaging) / EM (tomography)
-Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome
+Structural basis of the nucleosome transition during RNA polymerase II passage.
+Evolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes.
Science, Vol. 362, Issue 6413, Year 2018
David J F Ramrath / Moritz Niemann / Marc Leibundgut / Philipp Bieri / Céline Prange / Elke K Horn / Alexander Leitner / Daniel Boehringer / André Schneider / Nenad Ban
Methods: EM (single particle)
+ZNF598 Is a Quality Control Sensor of Collided Ribosomes.
Mol. Cell, Vol. 72, Issue 3, Page 469-481.e7, Year 2018
Szymon Juszkiewicz / Viswanathan Chandrasekaran / Zhewang Lin / Sebastian Kraatz / V Ramakrishnan / Ramanujan S Hegde
Methods: EM (single particle)
-About 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.
+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
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