-Browse 3DEM data
-Recently released data
-Mar 21, 2018 (EMDB: 28, PDB:16)
+Mar 14, 2018 (EMDB: 12, PDB:10)
+Mar 7, 2018 (EMDB: 9, PDB:5)Q: When the data are updated?
-Recent 3DEM papers
-Gating mechanisms of acid-sensing ion channels.
Nature, Vol. 555, Issue 7696, Page 397-401, Year 2018
Nate Yoder / Craig Yoshioka / Eric Gouaux
Methods: EM (single particle) / X-ray diffraction
-Structural basis for coupling protein transport and N-glycosylation at the mammalian endoplasmic reticulum.
Science, Year 2018
Katharina Braunger / Stefan Pfeffer / Shiteshu Shrimal / Reid Gilmore / Otto Berninghausen / Elisabet C Mandon / Thomas Becker / Friedrich Förster / Roland Beckmann
Methods: EM (subtomogram averaging) / EM (single particle)
+Atomic-level evidence for packing and positional amyloid polymorphism by segment from TDP-43 RRM2.
Nat. Struct. Mol. Biol., Year 2018
Elizabeth L Guenther / Peng Ge / Hamilton Trinh / Michael R Sawaya / Duilio Cascio / David R Boyer / Tamir Gonen / Z Hong Zhou / David S Eisenberg
Methods: EM (electron crystallography) / EM (helical sym.)
+The 3.5-Å CryoEM Structure of Nanodisc-Reconstituted Yeast Vacuolar ATPase VProton Channel.
Mol. Cell, Vol. 69, Issue 6, Page 993-1004.e3, Year 2018
Soung-Hun Roh / Nicholas J Stam / Corey F Hryc / Sergio Couoh-Cardel / Grigore Pintilie / Wah Chiu / Stephan Wilkens
Methods: EM (single particle)
+Structure of the nuclear exosome captured on a maturing preribosome.
-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 / EM Navigator (legacy version) / Yorodumi (legacy version)
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