[English] 日本語
Yorodumi Docs
- Documentation for Yorodumi, EM Navigator, Omokage, etc. -

-
Search & filter documents

-
News (18)

+
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
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.

PageDataFormat
EMN Searchsearch resultCSV, TSV, or JSON
EMN statisticsdata tableCSV 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.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
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

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.:Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession.
  • Enjoy "shape similarity" of biomolecules, more!

Related info.:Omokage search

+
Mar 3, 2016. Presentation PDF file for IPR seminar on Feb 19.

Presentation PDF file for IPR seminar on Feb 19.

External links:IPR seminar Feb 19th, 2016 / Presentation PDF

+
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

Related info.:Omokage search / gmfit

External links:Main text (HTML, Open Access) / Supplementray data (PDF, Open Access)

+
Nov 28, 2015. Omokage search starts to support SASBDB models

Omokage search starts to support SASBDB models

  • Models data in SASBDB are included in the Omokage search database.
    • SASBDB is a databank for small angle scattering data.
  • A SASBDB model can be used as a search query.
  • The search result may include SASBDB models.

Related info.:Omokage search / SASBDB / Comparison of 3 databanks

+
Dec 10, 2014. Multiple "PDB "SPLIT" entries are replaced with single "LARGE" entries

Multiple "PDB "SPLIT" entries are replaced with single "LARGE" entries

  • Structure data deposited as multiple PDB entries are replace with single combined entries, which were previously stored as "large structure".
  • In EM Navigator, many ribosome and several virus entries are replaced.

External links:Integration of Large Structures with the Main PDB Archive

+
Sep 22, 2014. New service: Omokage search

New service: Omokage search

  • Shape similarity search service, Omokage search has started.
  • 形状類似検索「Omokage検索」を開始しました。

Related info.:Omokage search

+
Mar 30, 2013. New page of EM Navigator, EMN Statistics

New page of EM Navigator, EMN Statistics

EMN Statistics

Related info.:EMN Statistics

+
Jan 16, 2013. New EMDB header format

New EMDB header format

  • Format of the EMDB header file (XML based meta data file, not the map data themselves) are updated to version 1.9.
  • Now, the contents of EM Navigator are based on the new data. Colors of some parts (e.g. bars in top area of the Detail pages) indicate 3D-reconstruction method, instead of "aggregation states".

External links:Announcement: EMDB header format update

-
FAQ (15)

+
Q: How do you make the images for the structure data? What do their colors mean?

A: Images of EMDB entries are made for EM Navigator, and ones of PDB entries are for Yorodumi. There are several patterns of coloring.

See following items for the details.

Related info.:Q: How do you make the movies in EM Navigator? / Q: How do you make the images of EMDB entries in Yorodumi, Omokage, etc.? / Q: How do you make the images of PDB entries in Yorodumi, Omokage, etc.?

+
Q: When the data are updated?

A: EMDB and PDB entries are released/updated every Wednesday at 0:00GMT/9:00JST

  • Data in EM Navigator, Yorodumi, and Omokage are updated at the same time.
  • SASBDB seems to update irregularly.

Related info.:Q: Where is the official data of EMDB?

External links:The release schedule of PDB data, the available data at each wwPDB site

+
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)

+
Q: Where is the official data of EMDB?

A: Following three are the official, have the same contents, and update at same time

CountryOrganizationHTTP URLFTP URL
JapanPDBjhttps://ftp.pdbj.org/pub/emdbftp://ftp.pdbj.org/pub/emdb
UKEBI PDBehttps://ftp.ebi.ac.uk/pub/databases/emdbftp://ftp.ebi.ac.uk/pub/databases/emdb
USAwwPDB & RCSB PDBhttps://ftp.wwpdb.org/pub/emdbftp://ftp.wwpdb.org/pub/emdb

Related info.:Q: When the data are updated?

External links:About the contents of the PDBj data site - PDBj

+
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)

Related info.:Q: What is the format for the maps? / EMDB map data format

External links:Kimura et al. Surface of bacteriorhodopsin revealed by high-resolution electron crystallography. Nature 389, 206, 1997 doi:10.1038/38323

+
Q: What is the format for the maps?

A: It is CCP4 map format

It's binary data with header for map geometry and body for density values.

Related info.:Q: Is an EM map electron-density map? / Q: Which software is suitable to view EMDB maps? / EMDB map data format

External links:EMDB Map Distribution Format Description (PDF document) / CCP4 map format

+
Q: Which software is suitable to view EMDB maps?

A: Many software packages can display CCP4 map data

Related info.:Q: What is the format for the maps? / Q: How do you make the movies in EM Navigator? / EMDB map data format

External links:UCSF Chimera Home Page

+
Q: What is EMD?

A: EMD (or emd) is "prefix" for ID number of EMDB

  • At the beginning, the EMDB was also called EMD.
  • Since the EM Navigator uses PDB and EMDB data, ID codes are indicated as [database name]-[ID], without the prefix. e.g. EMDB-1001, PDB-1brd.

Related info.:EMDB / EM Navigator / Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page) / ID/Accession-code notation in Yorodumi/EM Navigator

+
Q: What are the data sources of EM Navigator?

A: EMDB and PDB electron microscopy dat

  • Main source:
    • all EMDB entries
    • PDB entries with method information (exptl.details) including "electron microscopy" or "electron diffraction"
  • Some contents and infromation are original of EM Navigator:
    • Movies and their snapshot images
    • Projection and slice images
    • Some information about related data and similar structures

Related info.:EM Navigator / EMDB / PDB / EMN Search / EMN Papers / EMN Statistics

+
Q: Can I use the movies and their snapshots in the EM Navigator for papers or presentations?

A: Yes, plese

The EM Navigator movies and their snapshots are open to public. It would be appreciated if you would cite it as "EM Navigator, PDBj"

Related info.:Movie viewer

External links:Terms and conditions - PDBj

+
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 FFmpeg

  • 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

Related info.:Q: Which software is suitable to view EMDB maps? / Q: How do you make the images for the structure data? What do their colors mean? / Q: How do you make the images of EMDB entries in Yorodumi, Omokage, etc.? / Movie viewer / "Movies out of date"

External links:UCSF Chimera Home Page / Jmol: an open-source Java viewer for chemical structures in 3D / FFmpeg

+
Q: How do you make the images of EMDB entries in Yorodumi, Omokage, etc.?

A: in semi-automatic process with UCSF Chimera

  • Method:
    • We make been creating the images and movies for structure entries in EM Navigator using UCSF Chimera in semi-automatic process.
  • Orientation:
    • The structures are manually rotated to be seen in "good" orientation (usually, figures of the paper is refererd), or in similar orientation with similar structure data.
    • For the case of icosahedral symmetry structure data, they are viewed normal to their five-fold axis, while typical view of such the structure data are along the two-fold or three-fold axes. This is to unify the orientation with structure data with pseudo-icosahedral symmetry, such as bacteriophage with tail structures.
  • Color:
    • In EM Navigator, multiple images are made for a single entry. In Omokage search, image of "colored surface view" are shown.
    • The surface are colored by height, distance, or cylindrical radius. See the detail page for the coloring of particular images.

Related info.:Q: How do you make the images of PDB entries in Yorodumi, Omokage, etc.? / Q: How do you make the movies in EM Navigator? / Q: How do you make the images for the structure data? What do their colors mean?

External links:UCSF Chimera Home Page

+
Q: How do you make the images of PDB entries in Yorodumi, Omokage, etc.?

A: We are making them by full-automatic process using Jmol. Their styles are depend on the data type

  • Orientation:
    • Icosahedral assembly: Original orientation.
    • Helical assembly: 6 orientation (+/- of X, Y, Z direction) images are generated in jpeg format. Then, the largest file is chosen. (large JPEG => many dots/colors)
    • Others: by "rotate best" command of Jmol.
    • Ribosomes: by "rotate best" command of Jmol. Only RNA coordinates are used for the orientation.
  • Color:
    • monomer AUs: by N->C (blue->red) rainbow
    • BUs of monomer AUs: by "color molecule" (Jmol's coloring)
    • multimer AUs and thier BUs (including monomer BUs): by "color chain". For this coloring, Jmol uses not a rainbow color but the colors determined by the chain-ID.
  • Problems:
    • BU models are generated by Jmol's system. It works well for the most data, but there are some exception.
    • Checking and fixing processes of the many (>200,000) images are in progress. There are still some wrong images.

Related info.:Q: How do you make the images of EMDB entries in Yorodumi, Omokage, etc.?

External links:Jmol: an open-source Java viewer for chemical structures in 3D

+
Q: Who make these documents? Who develop EM Navigator, Yorodumi, Omokage search, etc?

A: Hirofumi Suzuki (PDBj / IPR, Osaka University)

Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.

Related info.:PDBj / Yorodumi annotation

External links:Contact to PDBj / Protein Data Bank Japan at IPR, Osaka-univ.

+
Q: What is difference in PDB coordinate formats?

A: As follows

FormatmmCIF compatibleFormat based onProviderComment
PDBx/mmCIF-CIF > STAR > plain textwwPDBOfficail data format
PDBnoplain textwwPDBLegacy officail
PDBMLyesXML > plain textwwPDBFor programers & develpers
PDBx/mmJSONyesJSON > plain textPDBjFor programers & develpers

Related info.:PDBx/mmCIF format / PDB format / PDBx/mmJSON format

-
Information (43)

+
EMDB map data format

3D density map data in CCP4 format

Related info.:EMDB / Q: What is the format for the maps? / Q: Which software is suitable to view EMDB maps? / Q: Is an EM map electron-density map?

External links:EMDB Map Distribution Format Description / Format technical details / CCP4 - Wikipedia

+
EMDB header

Meta information in XML format

Related info.:EMDB

External links:EMDB Schema v3 / EMDB Schema v1.9 / Documentation directory

+
Mask map

Map data of mask pattern, sub-region, segmentation, etc

Related info.:EMDB

+
FSC data file

Fourier shell correlation data in XML format for resolution estimation

Related info.:EMDB

External links:Fourier shell correlation - Wikipedia / FSC-schema

+
EMDB validaton report

Validaton report of EMDB entry by wwPDB and EMDB

Related info.:EMDB / wwPDB validaton report

External links:User guide to the EmDataBank map validation reports

+
PDBx/mmCIF format

Officail data format for PDB entries, in CIF text format, having atomic coordinates and meta information

Related info.:PDB / Q: What is difference in PDB coordinate formats?

External links:PDBx/mmCIF Dictionary Resources / Crystallographic Information File

+
PDB format

Legacy officail data format for PDB entries, contains atomic coordinates

Related info.:PDB / Q: What is difference in PDB coordinate formats?

External links:Atomic Coordinate Entry Format Version 3.3

+
PDBx/mmJSON format

JSON representation of the PDBx/mmCIF data developed by PDBj

Related info.:PDB / Q: What is difference in PDB coordinate formats?

External links:mmJSON - PDBj help

+
wwPDB validaton report

Validaton report of PDB entry by wwPDB

Related info.:PDB / EMDB validaton report

External links:wwPDB: Validation Reports / wwPDB: validation report FAQs

+
EM Navigator

3D electron microscopy data browser

URL: https://pdbj.org/emnavi/.

  • EM Navigator is a browser for 3D electron microscopy (3D-EM) data of biological molecules and assemblies.
  • It provides EMDB-PDB cross-search, statistical information, and links to similar structures.
  • You can easily check the latest EM structural data and structural papers.

Related info.:EMDB / PDB / PDBj / Q: What are the data sources of EM Navigator? / EMN Search / EMN Papers / EMN Gallery / EMN Statistics / Changes in new EM Navigator and Yorodumi

+
EMN Search

3DEM data search

URL: https://pdbj.org/emnavi/esearch.php

Advanced data search for EMDB and EM data in PDB widh various search and display options

Related info.:EMDB / PDB / EM Navigator / Q: What are the data sources of EM Navigator? / Yorodumi Search / Jul 5, 2019. Downlodablable text data

+
EMN Papers

Database of articles cited by 3DEM data entries

URL: https://pdbj.org/emnavi/pap.php?em=1

  • Database of articles cited by 3DEM data entries in EMDB and PDB
  • Using PubMed data

Related info.:EMDB / PDB / Q: What are the data sources of EM Navigator? / EM Navigator / Yorodumi Papers / Changes in new EM Navigator and Yorodumi

+
EMN Gallery

Image gallery of 3DEM data

URL: https://pdbj.org/emnavi/gallery.php

Categorization is done by EM Navigator manager manually. It is not strict.

Related info.:EM Navigator

+
EMN Statistics

Statistics of 3DEM data in table and graph styles

URL: https://pdbj.org/emnavi/stat.php

  • The table can be sorted. Click the column header to be sorted. (second click to reverse, [Shift]+click for multi-column sort)
  • To show the bar graph in table mode, point the column/row header by mouse courser.
  • To search the correspoinding data, click the cell of value.
  • Examples:

Related info.:Q: What are the data sources of EM Navigator? / EM Navigator / Mar 30, 2013. New page of EM Navigator, EMN Statistics

+
Yorodumi

Thousand views of thousand structures

URL: https://pdbj.org/emnavi/quick.php

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

+
Yorodumi Search

Cross-search of EMDB, PDB, SASBDB, etc.

URL: https://pdbj.org/emnavi/ysearch.php

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / EMN Search / Yorodumi / Experimental methods, equipments, and software data / Function and homology information / Changes in new EM Navigator and Yorodumi

+
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

URL: https://pdbj.org/emnavi/pap.php

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

+
Yorodumi Speices

Taxonomy data in EMDB/PDB/SASBDB

URL: https://pdbj.org/emnavi/taxo.php

Taxonomy database of sample sources of data in EMDB/PDB/SASBDB

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Mar 5, 2020. Novel coronavirus structure data

+
Omokage search

Search structure by SHAPE

URL: https://pdbj.org/omokage/

  • "Omokage search" is a shape similarity search service for 3D structures of macromolecules. By comparing global shapes, and ignoring details, similar-shaped structures are searched.
  • The search is performed ageinst >200,000 structure data, which consists of EMDB map data, PDB coordinates (deposited units (asymmetric units, usually), PDB biological units, and SASBDB mdoels).
  • For the search query, you can use either a data in the PDB/EMDB/SASBDB or your original model.
  • Supported formats are PDB (atomic model, SAXS bead model, etc.) and CCP4/MRC map (3D density map).
  • Shape comparison is performed by iDR profile method, which uses 1D-distance profiles of super-simplified models generated by vector quantizaion in Situs package.

Related info.:Comparison of 3 databanks / Sep 22, 2014. New service: Omokage search / gmfit / Re-ranking by gmfit

+
Yorodumi Docs

Documentation for Yorodumi, EM Navigator, Omokage, etc.

URL: https://pdbj.org/emnavi/doc.php

+
Covid-19 info

Page for Covid-19 featured contents

URL: https://pdbj.org/emnavi/covid19.php

Related info.:Comparison of 3 databanks / Aug 12, 2020. Covid-19 info

+
F&H Search

Function & Homology similarity search

URL: https://pdbj.org/emnavi/fh-search.php

Based on the similarity of Function & Homolog items related to the structure data, similar data are searched from structure databases.

Related info.:Function and homology information

+
Movie viewer

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.

Related info.:Q: How do you make the movies in EM Navigator? / Q: Can I use the movies and their snapshots in the EM Navigator for papers or presentations? / SurfView / Changes in new EM Navigator and Yorodumi

+
Jmol/JSmol

An open-source viewer for chemical structures in 3D

  • Mouse/touch operation
    X-Y rotationX-Y moveZoom in/out
    Mouseleft drag[Ctrl] + right dragcenter drag (vertical) / wheel
    Touchsingle fingerdouble fingerpinch
  • Jmol menu: [Ctrl] + click / right click

Related info.:Molmil / Yorodumi

External links:Jmol: an open-source Java viewer for chemical structures in 3D

+
Molmil

WebGL based molecular viewer

  • Molmil runs on Web browser on a smartphone or tablet device as well as PC. (Molmil is based on WebGL and Javascript).
  • Mouse/touch operation
    X-Y rotationX-Y moveZoom in/out
    Mouseleft dragcenter drag / shift + left dragright drag / wheel
    Touchsingle fingerdouble fingerpinch
  • Function menu: top left buttons on viewer screen

Related info.:Jmol/JSmol / SurfView / Changes in new EM Navigator and Yorodumi

External links:Documentation of Molmil in PDBj site / Molmil page in GitHub

+
SurfView

EMDB map surface models viewer on Web browsers

  • SurfView run on Web browser on a smartphone or tablet device as well as PC.
  • SurfView is based on a WebGL and three.js, Javascript 3D library.
  • The surface models shwon in this viewer are modified for simplification and data size reduction. To get views of full-resolution data, see movies instead.
  • Mouse/touch operation%table-1%

Related info.:Movie viewer / Molmil / Changes in new EM Navigator and Yorodumi

+
Comparison of 3 databanks

Yorodumi and Omokage can cross-search these DBs

MethodMain dataStr. data formatmeta data format
PDBvariousatomic modelPDBx/mmCIF, etc.PDBx/mmCIF, etc.
EMDB3DEM3D mapCCP4 mapEMDB XML
SASBDBSmall Angle Scattering (SAS)SAS profile
(+/- 3D models)
PDB + sasCIFASCII + sasCIF

Related info.:EMDB / PDB / SASBDB / Covid-19 info / ID/Accession-code notation in Yorodumi/EM Navigator / Experimental methods, equipments, and software data

+
ID/Accession-code notation in Yorodumi/EM Navigator

Databasepatterne.g.note
EMDBEMDB-****EMDB-1001prefix EMD- omitted
PDBPDB-****PDB-1a00
SASBDB_SASDA24as it is

Related info.:Comparison of 3 databanks / Q: What is EMD? / Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
EMDB

Electron Microscopy Data Bank, Databank for 3DEM

URL: https://www.ebi.ac.uk/emdb/

Related info.:3D electron microscopy (3DEM) / PDB / Comparison of 3 databanks

External links:The Electron Microscopy Data Bank - EBI / EMDataResource

+
PDB

Protein Data Bank - The single repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies

URL: https://wwPDB.org/

Related info.:PDBj / EMDB

+
PDBj

Protein Data Bank Japan

URL: http://pdbj.org/

A member of wwPDB

Related info.:PDB / Information from PDBMLplus

External links:Protein Data Bank Japan at IPR, Osaka-univ. / PDBj@Facebook / PDBj@Twitter

+
SASBDB

Small Angle Scattering Biological Data Bank - Curated repository for small angle scattering data and models

URL: http://www.sasbdb.org/

  • Develop & manage: BioSAXS group in EMBL
  • Since 2014

Related info.:Comparison of 3 databanks

External links:Valentini E, Kikhney AG, Previtali G, Jeffries CM, Svergun DI. SASBDB, a repository for biological small-angle scattering data. Nucleic Acids Res. 2015 Jan 28;43:D357-63.

+
gmfit

A program for fitting subunits into density map of complex using GMM (Gaussian Mixture Model)

URL: https://pdbj.org/gmfit/

  • Developed by Takeshi Kawabata in IPR, Osaka-univ.
  • Used from Omokage search.

Related info.:Omokage search / Dec 4, 2015. The article about Omokage search is published online / Re-ranking by gmfit

External links:Pairwise gmfit

+
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 statesMethods 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:
    AdvantageWider 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

The specimen is cooled at 4~100K (-269~-170℃) to keep it in hydrated state in the highly vaqumed environment, and to reduce radiation dammage by electron beam.

Related info.:3D electron microscopy (3DEM) / Q: Is 3DEM same as electron cryo microscopy (cryoEM)?

+
"Movies out of date"

Movies with this annotation may not be up-to-date.

EMDB map data are sometimes remediated. The process of making movies in the EM Navigaotr are not fully automated, and it is very hard to remake the all to catch up. So, some movies and movie parameters are based on the older data, and may be improper for new map data.

Related info.:Q: How do you make the movies in EM Navigator?

+
Carbohydrate representation

Polysaccaride/carbohydrate data representation in PDB

  • In July 2020, representation for polysaccaride/carbohydrate information in PDB is improved.
  • The polysaccaride figures are generated by GlycanBuilder2.
  • See following external links for details.

External links:Implementation of GlycanBuilder to draw a wide variety of ambiguous glycans - ScienceDirect / GlycanBuilder2 - RINGS (Resource For INformatics Of Glycomes at Soka) / Carbohydrate Remediation - wwPDB documentation / Coming July 29: Improved Carbohydrate Data at the PDB - wwPDB news

+
Experimental methods, equipments, and software data

Database of experimental methods of EMDB, PDB and SABDB.

URL: https://pdbj.org/emnavi/ysearch.php?&act_tab=met

Related info.:Comparison of 3 databanks / Yorodumi Search

+
Function and homology information

Molecular function, domain, and homology information from related databases.

  • To help to understand the molecular function and to find the related structure data, Yorodumi and Yorodumi Search display and utilize the related database information about function and homology.
  • In addition to the information of EC, EMBL, GeneBank, GO, InterPro, UniProt, etc. stored in the EMDB header XML, PDBx/mmCIF and sasCIF original data, information of Pfam, PROSITE, Reactome, UniProkKB, etc. are collected via PDBMLplus, EMDB-PDB fitting data, and/or UniProt.
    CategoryName of database or definition
    Function%Gene ontology, Enzyme Commission number, Reactome, etc.
    Domain/homologyCATH, InterPro, SMART, etc.
    ComponentUniProt, GenBank, PDB chemical component, etc.

Related info.:F&H Search / Information from PDBMLplus / Yorodumi Search / Yorodumi / F&H Search

+
Re-ranking by gmfit

The similarity ranking by Omokage search can be re-ordered according to correlation coefficient by gmfit, expecting incorporation of the (potential) benefits of two methods with following properties.

NameMethodSpeedPotential accuracy
Omokage searchiDR profile comparison++
sub-msec / 1 comparison
-
1D profile comparison
gmfitGaussian mixture model fitting+
sub-sec / 1 comparison
+
comparison in 3D space

Related info.:gmfit / Omokage search

+
Changes in new EM Navigator and Yorodumi

Changes in new versions of EM Navigator and Yorodumi. (Sep. 2016)

  • Changes:
    • 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.
    • The viewers (structure/movie viewers) appear in pop-up windows. On a PC, multiple viewer windows can be opened. On mobile devices, the viewers support touch operation.
  • New features:
    • Molmil, molecular structure viewer, and SurfView, surface model viewer for EMDB map data, are available to view the 3D structures. Both viewers support mobile device use.
    • Yorodumi support SASBDB entries.
    • Some new pages such as Yorodumi Papers, citation database of structure data entries and Yorodumi Search, cross search by keywords

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.

Related info.:PDBj / Function and homology information

External links:PDBMLplus - PDBj helip / About Functional Details page - PDBJ help

+
Yorodumi annotation

Annotation by Yorodumi/EM Navigator manager

Related info.:Q: Who make these documents? Who develop EM Navigator, Yorodumi, Omokage search, etc?

+
About Yorodumi Docs

-
Yorodumi Docs

Documentation for Yorodumi, EM Navigator, Omokage, etc.

Read more