[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleDynamics in cryo EM reconstructions visualized with maximum-likelihood derived variance maps.
Journal, issue, pagesJ Struct Biol, Vol. 181, Issue 3, Page 195-206, Year 2013
Publish dateDec 12, 2012
AuthorsQiu Wang / Tsutomu Matsui / Tatiana Domitrovic / Yili Zheng / Peter C Doerschuk / John E Johnson /
PubMed AbstractCryoEM data capture the dynamic character associated with biological macromolecular assemblies by preserving the various conformations of the individual specimens at the moment of flash freezing. ...CryoEM data capture the dynamic character associated with biological macromolecular assemblies by preserving the various conformations of the individual specimens at the moment of flash freezing. Regions of high variation in the data set are apparent in the image reconstruction due to the poor density that results from the lack of superposition of these regions. These observations are qualitative and, to date, only preliminary efforts have been made to quantitate the heterogeneity in the ensemble of particles that are individually imaged. We developed and tested a quantitative method for simultaneously computing a reconstruction of the particle and a map of the space-varying heterogeneity of the particle based on an entire data set. The method uses a maximum likelihood algorithm that explicitly takes into account the continuous variability from one instance to another instance of the particle. The result describes the heterogeneity of the particle as a variance to be plotted at every voxel of the reconstructed density. The test, employing time resolved data sets of virus maturation, not only recapitulated local variations obtained with difference map analysis, but revealed a remarkable time dependent reduction in the overall particle dynamics that was unobservable with classical methods of analysis.
External linksJ Struct Biol / PubMed:23246781 / PubMed Central
MethodsEM (single particle)
Resolution20.0 - 22.0 Å
Structure data

EMDB-5449:
Dynamics in Cryo EM Reconstructions Visualized with Maximum-Likelihood Derived Variance Maps
Method: EM (single particle) / Resolution: 22.0 Å

EMDB-5468:
Dynamics in Cryo EM Reconstructions Visualized with Maximum-Likelihood Derived Variance Maps
Method: EM (single particle)

EMDB-5469:
Dynamics in Cryo EM Reconstructions Visualized with Maximum-Likelihood Derived Variance Maps
Method: EM (single particle)

EMDB-5470:
Dynamics in Cryo EM Reconstructions Visualized with Maximum-Likelihood Derived Variance Maps
Method: EM (single particle)

EMDB-5471:
Dynamics in Cryo EM Reconstructions Visualized with Maximum-Likelihood Derived Variance Maps
Method: EM (single particle)

EMDB-5472:
Dynamics in Cryo EM Reconstructions Visualized with Maximum-Likelihood Derived Variance Maps
Method: EM (single particle) / Resolution: 21.0 Å

EMDB-5473:
Dynamics in Cryo EM Reconstructions Visualized with Maximum-Likelihood Derived Variance Maps
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-5474:
Dynamics in Cryo EM Reconstructions Visualized with Maximum-Likelihood Derived Variance Maps
Method: EM (single particle) / Resolution: 21.0 Å

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
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

+
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

+
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

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • 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

Read more