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

Meta information in XML format

Data file in XML format containing information associated with the map of EMDB entries, experimental information, detailed sample information, etc.

Related info.:EMDB / Feb 9, 2022. New format data for meta-information of EMDB entries

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

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

Related info.:EMDB

Fourier shell correlation data in XML format for resolution estimation

Related info.:EMDB

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

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

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

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

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

Validaton report of PDB entry by wwPDB

Related info.:PDB / EMDB validaton report

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

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.

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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

Database of articles cited by 3DEM data entries

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

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Image gallery of 3DEM data

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

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Statistics of 3DEM data in table and graph styles

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

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.

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

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

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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

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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

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

Documentation for Yorodumi, EM Navigator, Omokage, etc.

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

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

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

Visualization of 3DEM structure data by movies

• Horizontal- and vertical- rotation motions and "slicing" motion are recorded in the movies.
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An open-source viewer for chemical structures in 3D

• Mouse/touch operation

  	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

• Jmol menu: [Ctrl] + click / right click

Related info.:Molmil / Yorodumi

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

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 rotation	X-Y move	Zoom in/out
  Mouse	left drag	center drag / shift + left drag	right drag / wheel
  Touch	single finger	double finger	pinch

• 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

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

Yorodumi and Omokage can cross-search these DBs

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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)

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

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

Protein Data Bank Japan

URL: http://pdbj.org/

A member of wwPDB

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

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.

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

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

EMDB map data are sometimes remediated. The process of making movies in the EM Navigator 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?

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

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

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.

  Category	Name of database or definition
  Function%	Gene ontology, Enzyme Commission number, Reactome, etc.
  Domain/homology	CATH, InterPro, SMART, etc.
  Component	UniProt, GenBank, PDB chemical component, etc.

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

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.

Related info.:gmfit / Omokage search

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

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

Annotation by Yorodumi/EM Navigator manager

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