[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

TitleCryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome.
Journal, issue, pagesNucleic Acids Res, Vol. 51, Issue 17, Page 8909-8924, Year 2023
Publish dateSep 22, 2023
AuthorsYing-Hui Wang / Hong Dai / Ling Zhang / Yun Wu / Jingfen Wang / Chen Wang / Cai-Huang Xu / Hai Hou / Bing Yang / Yongqun Zhu / Xing Zhang / Jie Zhou /
PubMed AbstractArchaeal ribosomes have many domain-specific features; however, our understanding of these structures is limited. We present 10 cryo-electron microscopy (cryo-EM) structures of the archaeal ribosome ...Archaeal ribosomes have many domain-specific features; however, our understanding of these structures is limited. We present 10 cryo-electron microscopy (cryo-EM) structures of the archaeal ribosome from crenarchaeota Sulfolobus acidocaldarius (Sac) at 2.7-5.7 Å resolution. We observed unstable conformations of H68 and h44 of ribosomal RNA (rRNA) in the subunit structures, which may interfere with subunit association. These subunit structures provided models for 12 rRNA expansion segments and 3 novel r-proteins. Furthermore, the 50S-aRF1 complex structure showed the unique domain orientation of aRF1, possibly explaining P-site transfer RNA (tRNA) release after translation termination. Sac 70S complexes were captured in seven distinct steps of the tRNA translocation reaction, confirming conserved structural features during archaeal ribosome translocation. In aEF2-engaged 70S ribosome complexes, 3D classification of cryo-EM data based on 30S head domain identified two new translocation intermediates with 30S head domain tilted 5-6° enabling its disengagement from the translocated tRNA and its release post-translocation. Additionally, we observed conformational changes to aEF2 during ribosome binding and switching from three different states. Our structural and biochemical data provide new insights into archaeal translation and ribosome translocation.
External linksNucleic Acids Res / PubMed:37604686 / PubMed Central
MethodsEM (single particle)
Resolution2.72 - 5.72 Å
Structure data

EMDB-34860, PDB-8hku:
Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
Method: EM (single particle) / Resolution: 2.72 Å

EMDB-34861, PDB-8hkv:
Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
Method: EM (single particle) / Resolution: 4.94 Å

EMDB-34862, PDB-8hkx:
Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
Method: EM (single particle) / Resolution: 3.14 Å

EMDB-34863, PDB-8hky:
Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
Method: EM (single particle) / Resolution: 4.45 Å

EMDB-34864, PDB-8hkz:
Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
Method: EM (single particle) / Resolution: 4.78 Å

EMDB-34866, PDB-8hl1:
Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
Method: EM (single particle) / Resolution: 3.93 Å

EMDB-34867, PDB-8hl2:
Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
Method: EM (single particle) / Resolution: 4.1 Å

EMDB-34868, PDB-8hl3:
Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
Method: EM (single particle) / Resolution: 4.8 Å

EMDB-34869, PDB-8hl4:
Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
Method: EM (single particle) / Resolution: 4.62 Å

EMDB-34870, PDB-8hl5:
Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
Method: EM (single particle) / Resolution: 5.72 Å

Chemicals

ChemComp-UNK:
UNKNOWN

ChemComp-GNP:
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp, GMPPNP, energy-carrying molecule analogue*YM

Source
  • sulfolobus acidocaldarius dsm 639 (acidophilic)
KeywordsRIBOSOME / Sulfolobus acidocaldarius ribosome small subunit / Sulfolobus acidocaldarius ribosome

+
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