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+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
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+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.
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- 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
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+Aug 31, 2016. New EM Navigator & Yorodumi
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+Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.
+Dec 4, 2015. The article about Omokage search is published online
The article about Omokage search is published online
- Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB. Suzuki Hirofumi, Kawabata Takeshi, and Nakamura Haruki, Bioinformatics. (2015) btv614
main text (HTML, Open Access), supplementray data (PDF, Open Access)
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+Nov 28, 2015. Omokage search starts to support SASBDB models
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+Dec 10, 2014. PDB "SPLIT" entries are replaced with "LARGE" entries
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+Q: How do you make the images for the structure data? What do their colors mean?
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+Q: Is 3DEM same as electron cryo microscopy (cryoEM)?
A: No, "3DEM" and "cryoEM" are distinct to be exact.
- However, they are closely related. Some people call 3DEM "cryoEM
- Many but not all the 3DEM analyses are perfomed with cryoEM. In EMDB and PDB, there are some entries, whose structure data were obtained in non-cryo contition.
Related info.:3D electron microscopy (3DEM) / electron cryo microscopy (cryoEM)
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Country Organization URL Japan PDBj ftp://ftp.pdbj.org/pub/emdb UK EBI ftp://ftp.ebi.ac.uk/pub/databases/emdb USA wwPDB ftp://ftp.wwpdb.org/pub/emdb
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+Q: Is an EM map electron-density map?
A: No. But, they are very similar.
- To be exact, 3D map derived by 3D-EM is related to Coulomb potential (or electron potential), rather than electron density.
- The difference seems to be ignored in the most studies of atomic model building and fitting.
- Thers are some reports that protonation state affects the density. (see the ext. link)
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+Q: What is the format for the maps?
A: It is CCP4 map format
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- Here is description of EMDB map data. EMDB_map_Format.pdf
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External links:CCP4 map format
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A: EMD (or emd) is "prefix" for ID number of EMDB
- At the beginning, the EMDB was also called EMD.
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+Q: What is the data source of EM Navigator?
A: EMDB and PDB electron microscopy data
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+Q: How do you make the movies in EM Navigator?
A: Series of images are recorded by UCSF-Chimera or Jmol. Then, they are encoded into movie files by avconv command in the libav package.
- This is an example of Chimera script.
system mkdir img1 movie reset movie record fformat png directory ./img1/ pattern img* roll y 2 180; wait wait 15 roll x 2 180; wait reset pos1; wait reset pos2 180; wait reset pos1 180; wait reset movie stop("pos1" and "pos2" are saved position, which are the start and end of sectioning motion)
- Chimera session files distributed with the movie files may be helpfull.
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A: We are making them by full-automatic process using Jmol. Their styles are depend on the data type
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- Others: by "rotate best" command of Jmol.
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- monomer AUs: by N->C (blue->red) rainbow
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3D electron microscopy data browser
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Statistics of 3DEM data in table and graph styles
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Related info.:Comparison of 3 databanks / Aug 12, 2020. New: Covid-19 info
Visualization of 3DEM structure data by movies.
- Horizontal- and vertical- rotation motions and "slicing" motion are recorded in the movies.
- As the movie frame can be controlled by mouse/touch position, it can be operated interactively as a molecular viewer. According to the mouse/finger position and orientation of the motion on the movie panel, the model rotates on horizontal or vertical direction. By horizontal mouse/finger movement on the top part of the movie, the slicing motion is shown.
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An open-source viewer for chemical structures in 3D
|X-Y rotation||X-Y move||Zoom in/out|
|Mouse||left drag||[Ctrl] + right drag||center drag (vertical) / wheel|
|Touch||single finger||double finger||pinch|
Related info.:Molmil / Yorodumi
+3D electron microscopy (3DEM)
A generic term of electron microscopic analyses to obtain 3D structures
- Analyses such as electron tomography, single particle analysis, and electron diffraction are included.
Aggregation states Methods generally used "individual structure" electron tomography "single particle" single particle analysis "icosahedral" single particle analysis "helical" helical reconstruction / single particle analysis "2D/3D-crystal" electron diffraction / Fourier filtering
- Characteristics compared to X-ray crystallography and NMR:
- Advantage: Wider applicability of sample (not require high-purity or high-concentration smaple, and useful for more huge, complex, flexible, and less uniform sample)
- Disadvantage (previous): Lower resolution (hard to get atomic-level resolution data)
- Disadvantage (new): High-performance electron microscopes and their maintenance costs are quite expensive.
Related info.:EMDB / electron cryo microscopy (cryoEM)
+electron cryo microscopy (cryoEM)
Electron microscopy where the sample is studied at cryogenic temperatures
Related info.:3D electron microscopy (3DEM) / Q: Is 3DEM same as electron cryo microscopy (cryoEM)?
External links:Cryo-electron microscopy - Wikipedia
+"Movies out of date"
Movies with this annotation may not be up-to-date.
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+Changes in new EM Navigator and Yorodumi
Changes in new versions of EM Navigator and Yorodumi. (Sep. 2016)
- New user interface unified in EM Navigator, Yorodumi & Omokage search, supporting mobile devices as well as PCs.
- New Yorodumi replace the individual data page ("Detail page" of EM Navigator in the legacy system). It is unified browser for EMDB, PDB, and SASBDB entries integrated with EM Navigator and Omokage search.
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Related info.:EM Navigator / Yorodumi / SurfView / Molmil / Movie viewer / EMN Papers / Yorodumi Papers / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi
+Information from PDBMLplus
PDBMLplus is the XML format file including additional information relating to individual proteins. Currently, PDB files are lacking a detailed description of function, experimental conditions, and the like. And then such information was included to extended XML database, named PDBMLplus.
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