-Browse 3DEM data
-Recently released data
All new data for the week / Advanced search
Covid-19 / SARS-CoV-2 / Advanced search / Covid-19 info
DNA or RNA, (replication, transcription, etc.) / Advanced search
Ribosome & component / Advanced search
Protein folding and degradation / Advanced search
Membrane protein, pore forming, transformation / Advanced search
Cytoskeleton & motor / Advanced search
Virus & component / Advanced search
Others / Advanced search
-Recent 3DEM papers
-Structural basis of malaria RIFIN binding by LILRB1-containing antibodies.
Nature, Year 2021
Yiwei Chen / Kai Xu / Luca Piccoli / Mathilde Foglierini / Joshua Tan / Wenjie Jin / Jason Gorman / Yaroslav Tsybovsky / Baoshan Zhang / Boubacar Traore ...Yiwei Chen / Kai Xu / Luca Piccoli / Mathilde Foglierini / Joshua Tan / Wenjie Jin / Jason Gorman / Yaroslav Tsybovsky / Baoshan Zhang / Boubacar Traore / Chiara Silacci-Fregni / Claudia Daubenberger / Peter D Crompton / Roger Geiger / Federica Sallusto / Peter D Kwong / Antonio Lanzavecchia
Methods: EM (single particle)
-The myosin II coiled-coil domain atomic structure in its native environment.
Proc Natl Acad Sci U S A, Vol. 118, Issue 14, Year 2021
Hamidreza Rahmani / Wen Ma / Zhongjun Hu / Nadia Daneshparvar / Dianne W Taylor / J Andrew McCammon / Thomas C Irving / Robert J Edwards / Kenneth A Taylor
Methods: EM (single particle)
+Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography.
Nat Commun, Vol. 12, Issue 1, Page 1957, Year 2021
Jonathan Bouvette / Hsuan-Fu Liu / Xiaochen Du / Ye Zhou / Andrew P Sikkema / Juliana da Fonseca Rezende E Mello / Bradley P Klemm / Rick Huang / Roel M Schaaper / Mario J Borgnia / Alberto Bartesaghi
Methods: EM (single particle) / EM (subtomogram averaging)
+The multi-scale architecture of mammalian sperm flagella and implications for ciliary motility.
EMBO J, Vol. 40, Issue 7, Page e107410, Year 2021
Miguel Ricardo Leung / Marc C Roelofs / Ravi Teja Ravi / Paula Maitan / Heiko Henning / Min Zhang / Elizabeth G Bromfield / Stuart C Howes / Bart M Gadella / Hermes Bloomfield-Gadêlha / Tzviya Zeev-Ben-Mordehai
Methods: EM (subtomogram averaging)
+Near-atomic structure of an atadenovirus reveals a conserved capsid-binding motif and intergenera variations in cementing proteins.
-About EM Navigator
-Aug 12, 2020. New: Covid-19 info
New: Covid-19 info
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info
+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
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