[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

TitleReconstruction of the ancient cyanobacterial proto-circadian clock system KaiABC.
Journal, issue, pagesEMBO J, Vol. 44, Issue 10, Page 3025-3046, Year 2025
Publish dateApr 10, 2025
AuthorsSilin Li / Zengxuan Zhou / Yufeng Wan / Xudong Jia / Peiliang Wang / Yu Wang / Taisen Zuo / He Cheng / Xiaoting Fang / Shuqi Dong / Jun He / Yilin Yang / Yichen Xu / Shaoxuan Fu / Xujing Wang / Ximing Qin / Qiguang Xie / Xiaodong Xu / Yuwei Zhao / Dan Liang / Peng Zhang / Qinfen Zhang / Jinhu Guo /
PubMed AbstractEarlier in its history, the Earth used to spin faster than it does today. How ancient organisms adapted to the short day/night cycles during that time remains unclear. In this study we reconstruct ...Earlier in its history, the Earth used to spin faster than it does today. How ancient organisms adapted to the short day/night cycles during that time remains unclear. In this study we reconstruct and analyse the ancient circadian clock system KaiABC (anKaiABC) of cyanobacteria that existed ~0.95 billion years ago, when the daily light/dark cycle was ~18 h-long. Compared to their contemporary counterparts, anKaiABC proteins had different structures and interactions. The kinase, phosphatase, and adenosine triphosphatase (ATPase) activities of anKaiC were lower, while the anKaiA and anKaiB proteins were less effective at regulating the KaiC/anKaiC phosphorylation status. We provide evidence indicating that the anKaiABC system does not endogenously oscillate, but it can be entrained by an 18 h-long light/dark cycle. A Synechococcus strain expressing ankaiABC genes exhibits better adaptation to 9-h light/9-h dark cycles (LD9:9) that mimic the ancient 18-h day/night cycles, whereas the kaiABC-expressing strain preferentially adapts to the LD12:12 contemporary conditions. These findings suggest that, despite its lack of self-sustaining circadian oscillation, the proto-circadian system may have mediated adaptation of ancient cyanobacteria to the 18 h-long light/dark cycles present 0.95 billion years ago.
External linksEMBO J / PubMed:40210722 / PubMed Central
MethodsEM (single particle)
Resolution2.51 Å
Structure data

36461

8jon

EMDB-36461, PDB-8jon:
Structure of a synthetic circadian clock protein KaiC mutant of cyanobacteria Synechococcus elongatus PCC 7942
Method: EM (single particle) / Resolution: 2.51 Å

Chemicals

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

Source
  • synechococcus elongatus (strain atcc 33912 / pcc 7942 / fachb-805) (bacteria)
KeywordsBIOSYNTHETIC PROTEIN / circadian clock protein / Synthetic protein / KaiC

+
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