8JON | pdb_00008jon

Structure of a synthetic circadian clock protein KaiC mutant of cyanobacteria Synechococcus elongatus PCC 7942


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.51 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Reconstruction of the ancient cyanobacterial proto-circadian clock system KaiABC.

Li, S.Zhou, Z.Wan, Y.Jia, X.Wang, P.Wang, Y.Zuo, T.Cheng, H.Fang, X.Dong, S.He, J.Yang, Y.Xu, Y.Fu, S.Wang, X.Qin, X.Xie, Q.Xu, X.Zhao, Y.Liang, D.Zhang, P.Zhang, Q.Guo, J.

(2025) EMBO J 44: 3025-3046

  • DOI: https://doi.org/10.1038/s44318-025-00425-0
  • Primary Citation of Related Structures:  
    8JON

  • PubMed Abstract: 

    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.


  • Organizational Affiliation
    • School of Life Sciences, Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Circadian clock oscillator protein KaiC
A, B, C, D, E
A, B, C, D, E, F
524Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
Gene Names: kaiCSynpcc7942_1216see0011
EC: 2.7.11.1 (PDB Primary Data), 3.6.4 (PDB Primary Data)
UniProt
Find proteins for Q79PF4 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore Q79PF4 
Go to UniProtKB:  Q79PF4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ79PF4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
AA [auth F]
G [auth A]
K [auth B]
O [auth C]
S [auth D]
AA [auth F],
G [auth A],
K [auth B],
O [auth C],
S [auth D],
W [auth E]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
CA [auth F]
I [auth A]
M [auth B]
Q [auth C]
U [auth D]
CA [auth F],
I [auth A],
M [auth B],
Q [auth C],
U [auth D],
Y [auth E]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BA [auth F]
DA [auth F]
H [auth A]
J [auth A]
L [auth B]
BA [auth F],
DA [auth F],
H [auth A],
J [auth A],
L [auth B],
N [auth B],
P [auth C],
R [auth C],
T [auth D],
V [auth D],
X [auth E],
Z [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.51 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-12
    Type: Initial release
  • Version 1.1: 2025-07-23
    Changes: Advisory, Data collection, Derived calculations, Structure summary
  • Version 1.2: 2025-12-31
    Changes: Data collection, Database references, Structure summary