[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

TitleMiLoPYP: self-supervised molecular pattern mining and particle localization in situ.
Journal, issue, pagesNat Methods, Vol. 21, Issue 10, Page 1863-1872, Year 2024
Publish dateSep 9, 2024
AuthorsQinwen Huang / Ye Zhou / Alberto Bartesaghi /
PubMed AbstractCryo-electron tomography allows the routine visualization of cellular landscapes in three dimensions at nanometer-range resolutions. When combined with single-particle tomography, it is possible to ...Cryo-electron tomography allows the routine visualization of cellular landscapes in three dimensions at nanometer-range resolutions. When combined with single-particle tomography, it is possible to obtain near-atomic resolution structures of frequently occurring macromolecules within their native environment. Two outstanding challenges associated with cryo-electron tomography/single-particle tomography are the automatic identification and localization of proteins, tasks that are hindered by the molecular crowding inside cells, imaging distortions characteristic of cryo-electron tomography tomograms and the sheer size of tomographic datasets. Current methods suffer from low accuracy, demand extensive and time-consuming manual labeling or are limited to the detection of specific types of proteins. Here, we present MiLoPYP, a two-step dataset-specific contrastive learning-based framework that enables fast molecular pattern mining followed by accurate protein localization. MiLoPYP's ability to effectively detect and localize a wide range of targets including globular and tubular complexes as well as large membrane proteins, will contribute to streamline and broaden the applicability of high-resolution workflows for in situ structure determination.
External linksNat Methods / PubMed:39251798 / PubMed Central
MethodsEM (subtomogram averaging)
Resolution5.0 - 37.0 Å
Structure data

EMDB-45261: CryoEM reconstruction of 70S ribosome from EMPIAR-10304
Method: EM (subtomogram averaging) / Resolution: 5.0 Å

EMDB-45266: Structure of 70S ribosome from EMPIAR-10499
Method: EM (subtomogram averaging) / Resolution: 5.4 Å

EMDB-45267: Open state SARS-COV2 spike protein from EMPIAR-10453
Method: EM (subtomogram averaging) / Resolution: 5.6 Å

EMDB-45268: Structure of closed state SARS-Cov2 spike protein from EMPIAR-10453
Method: EM (subtomogram averaging) / Resolution: 9.3 Å

EMDB-45269: Structure of RuBisCO from EMPIAR-10694
Method: EM (subtomogram averaging) / Resolution: 13.0 Å

EMDB-45270: Structure of 80S ribosome from EMPIAR-10987
Method: EM (subtomogram averaging) / Resolution: 8.6 Å

EMDB-45271: Structure of microtubule from EMPIAR-10987
Method: EM (subtomogram averaging) / Resolution: 37.0 Å

EMDB-45272: Structure of ATP synthase from EMPIAR-11658
Method: EM (subtomogram averaging) / Resolution: 13.0 Å

Source
  • Escherichia coli DH5[alpha] (bacteria)
  • Mycoplasmoides pneumoniae 19294 (bacteria)
  • Chlamydomonas reinhardtii (plant)
  • Mus musculus (house mouse)
  • Saccharomyces cerevisiae (brewer's yeast)

+
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