Extended conformation of daytime state KaiC

Experimental Data Snapshot

  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Coupling of distant ATPase domains in the circadian clock protein KaiC.

Swan, J.A.Sandate, C.R.Chavan, A.G.Freeberg, A.M.Etwaru, D.Ernst, D.C.Palacios, J.G.Golden, S.S.LiWang, A.Lander, G.C.Partch, C.L.

(2022) Nat Struct Mol Biol 29: 759-766

  • DOI: https://doi.org/10.1038/s41594-022-00803-w
  • Primary Citation of Related Structures:  
    7S65, 7S66, 7S67

  • PubMed Abstract: 

    The AAA + family member KaiC is the central pacemaker for circadian rhythms in the cyanobacterium Synechococcus elongatus. Composed of two hexameric rings of adenosine triphosphatase (ATPase) domains with tightly coupled activities, KaiC undergoes a cycle of autophosphorylation and autodephosphorylation on its C-terminal (CII) domain that restricts binding of clock proteins on its N-terminal (CI) domain to the evening. Here, we use cryogenic-electron microscopy to investigate how daytime and nighttime states of CII regulate KaiB binding on CI. We find that the CII hexamer is destabilized during the day but takes on a rigidified C 2 -symmetric state at night, concomitant with ring-ring compression. Residues at the CI-CII interface are required for phospho-dependent KaiB association, coupling ATPase activity on CI to cooperative KaiB recruitment. Together, these studies clarify a key step in the regulation of cyanobacterial circadian rhythms by KaiC phosphorylation.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Circadian clock protein kinase KaiC
A, B, C, D, E
A, B, C, D, E, F
519Synechococcus elongatusMutation(s): 2 
Gene Names: kaiCSynpcc7942_1216see0011
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
  • 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 
BA [auth F]
G [auth A]
K [auth A]
M [auth B]
Q [auth C]
BA [auth F],
G [auth A],
K [auth A],
M [auth B],
Q [auth C],
U [auth D]
C10 H16 N5 O13 P3
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
CA [auth F]
I [auth A]
O [auth B]
S [auth C]
W [auth D]
CA [auth F],
I [auth A],
O [auth B],
S [auth C],
W [auth D],
Z [auth E]
C10 H15 N5 O10 P2
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AA [auth E]
DA [auth F]
H [auth A]
J [auth A]
L [auth A]
AA [auth E],
DA [auth F],
H [auth A],
J [auth A],
L [auth A],
N [auth B],
P [auth B],
R [auth C],
T [auth C],
V [auth D],
X [auth D],
Y [auth E]
Experimental Data & Validation

Experimental Data

  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesR21GM142196

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-22
    Type: Initial release
  • Version 1.1: 2022-07-27
    Changes: Database references
  • Version 1.2: 2022-08-03
    Changes: Database references
  • Version 1.3: 2022-08-24
    Changes: Database references