[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

TitleVisualizing ribosome biogenesis: parallel assembly pathways for the 30S subunit.
Journal, issue, pagesScience, Vol. 330, Issue 6004, Page 673-677, Year 2010
Publish dateOct 29, 2010
AuthorsAnke M Mulder / Craig Yoshioka / Andrea H Beck / Anne E Bunner / Ronald A Milligan / Clinton S Potter / Bridget Carragher / James R Williamson /
PubMed AbstractRibosomes are self-assembling macromolecular machines that translate DNA into proteins, and an understanding of ribosome biogenesis is central to cellular physiology. Previous studies on the ...Ribosomes are self-assembling macromolecular machines that translate DNA into proteins, and an understanding of ribosome biogenesis is central to cellular physiology. Previous studies on the Escherichia coli 30S subunit suggest that ribosome assembly occurs via multiple parallel pathways rather than through a single rate-limiting step, but little mechanistic information is known about this process. Discovery single-particle profiling (DSP), an application of time-resolved electron microscopy, was used to obtain more than 1 million snapshots of assembling 30S subunits, identify and visualize the structures of 14 assembly intermediates, and monitor the population flux of these intermediates over time. DSP results were integrated with mass spectrometry data to construct the first ribosome-assembly mechanism that incorporates binding dependencies, rate constants, and structural characterization of populated intermediates.
External linksScience / PubMed:21030658 / PubMed Central
MethodsEM (single particle)
Resolution31.67 - 66.12 Å
Structure data

EMDB-1783:
30S Ribosome Subunit Assembly Intermediates
Method: EM (single particle)

EMDB-2453:
30S Ribosome Subunit Assembly Intermediates, Intermediate Group 4a
Method: EM (single particle) / Resolution: 31.67 Å

EMDB-2454:
30S Ribosome Subunit Assembly Intermediates, Intermediate Group 4b
Method: EM (single particle) / Resolution: 40.87 Å

EMDB-2455:
30S Ribosome Subunit Assembly Intermediates, Intermediate 4c
Method: EM (single particle) / Resolution: 47.07 Å

EMDB-2456:
30S Ribosome Subunit Assembly Intermediates, Intermediate Group 4d
Method: EM (single particle) / Resolution: 43.02 Å

EMDB-2457:
30S Ribosome Subunit Assembly Intermediates, Intermediate Group 4e
Method: EM (single particle) / Resolution: 46.21 Å

EMDB-2458:
30S Ribosome Subunit Assembly Intermediates, Intermediate Group1b
Method: EM (single particle) / Resolution: 59.04 Å

EMDB-2460:
30S Ribosome Subunit Assembly Intermediates, Intermediate Group 1a
Method: EM (single particle) / Resolution: 66.12 Å

EMDB-2461:
30S Ribosome Subunit Assembly Intermediates, Intermediate Group 2a
Method: EM (single particle) / Resolution: 53.42 Å

EMDB-2465:
30S Ribosome Subunit Assembly Intermediates, Intermediate Group 2b
Method: EM (single particle) / Resolution: 55.63 Å

EMDB-2466:
30S Ribosome Subunit Assembly Intermediates, Intermediate Group 2c
Method: EM (single particle) / Resolution: 45.94 Å

EMDB-2467:
30S Ribosome Subunit Assembly Intermediates, Intermediate Group 3a
Method: EM (single particle) / Resolution: 39.94 Å

EMDB-2468:
30S Ribosome Subunit Assembly Intermediates, Intermediate Group 3b
Method: EM (single particle) / Resolution: 44.04 Å

EMDB-2469:
30S Ribosome Subunit Assembly Intermediates, Intermediate Group 3c
Method: EM (single particle) / Resolution: 51.0 Å

EMDB-2470:
30S Ribosome Subunit Assembly Intermediates, Intermediate Group 4f
Method: EM (single particle) / Resolution: 32.73 Å

Source
  • Escherichia coli (E. coli)

+
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