Overall structure of fully assembled cyanobacterial KaiABC circadian clock complex by an integrated experimental-computational approach.

Yunoki Y, Matsumoto A, Morishima K, Martel A, Porcar L, Sato N, Yogo R, Tominaga T, Inoue R, Yagi-Utsumi M, Okuda A, Shimizu M, Urade R, Terauchi K, Kono H, Yagi H, Kato K, Sugiyama M, Commun Biol 5(1):184 (2022) Europe PMC

SASDNK2 – Circadian clock hKaiA-75dKaiB-75dKaiC ternary protein complex measured by SEC-SANS in 100% D2O

75% deuterated Circadian clock protein KaiB
Circadian clock protein KaiA
75% deuterated Circadian clock protein kinase KaiC (S431D mutant)
MWexperimental 810 kDa
MWexpected 821 kDa
VPorod 1620 nm3
log I(s) 3.12×10-1 3.12×10-2 3.12×10-3 3.12×10-4
75% deuterated Circadian clock protein KaiB Circadian clock protein KaiA 75% deuterated Circadian clock protein kinase KaiC (S431D mutant) small angle scattering data  s, nm-1
ln I(s)
75% deuterated Circadian clock protein KaiB Circadian clock protein KaiA 75% deuterated Circadian clock protein kinase KaiC (S431D mutant) Guinier plot ln 3.12×10-1 Rg: 7.8 nm 0 (7.8 nm)-2 s2
(sRg)2I(s)/I(0)
75% deuterated Circadian clock protein KaiB Circadian clock protein KaiA 75% deuterated Circadian clock protein kinase KaiC (S431D mutant) Kratky plot 1.104 0 3 sRg
p(r)
75% deuterated Circadian clock protein KaiB Circadian clock protein KaiA 75% deuterated Circadian clock protein kinase KaiC (S431D mutant) pair distance distribution function Rg: 8.2 nm 0 Dmax: 25.6 nm

Data validation


Fits and models


log I(s)
 s, nm-1
75% deuterated Circadian clock protein KaiB Circadian clock protein KaiA 75% deuterated Circadian clock protein kinase KaiC (S431D mutant) OTHER model

log I(s)
 s, nm-1
75% deuterated Circadian clock protein KaiB Circadian clock protein KaiA 75% deuterated Circadian clock protein kinase KaiC (S431D mutant) OTHER model

SANS data from solutions of the circadian clock hKaiA-75dKaiB-75dKaiC ternary protein complex in 50 mM sodium phosphate buffer, 150 mm NaCl, 5 mM MgCl2, 0.5 mM EDTA, 1 mM ATP, 1 mM DTT, 50 mM arginine, 50 mM glutamine, in 100% D2O, pD 7.8 were collected using the D22 SANS instrument at the ILL (Grenoble, France) equipped with a Reuter-Stokes 3He detector at a sample-detector distance of 5.6 m and at a wavelength of λ = 0.6 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SANS was employed. The SEC parameters were as follows: A sample was injected onto a column at 25°C. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

The molecular weight was determined by analytical ultracentrifugation (AUC). SEC column and SEC parameters: UNKNOWN. Neutron exposure time: UNKNOWN.

75% deuterated Circadian clock protein KaiB
Mol. type   Protein
Organism   Synechococcus elongatus (strain PCC 7942 / FACHB-805)
Olig. state   Hexamer
Mon. MW   11.8 kDa
 
UniProt   Q79PF5 (1-102)
Sequence   FASTA
 
Circadian clock protein KaiA
Mol. type   Protein
Organism   Synechococcus elongatus (strain PCC 7942 / FACHB-805)
Olig. state   Dodecamer
Mon. MW   32.8 kDa
 
UniProt   Q79PF6 (1-284)
Sequence   FASTA
 
75% deuterated Circadian clock protein kinase KaiC (S431D mutant)
Mol. type   Protein
Organism   Synechococcus elongatus (strain PCC 7942 / FACHB-805)
Olig. state   Hexamer
Mon. MW   59.5 kDa
 
UniProt   Q79PF4 (1-519)
Sequence   FASTA