Biological Assembly 1  

Global Symmetry: Dihedral - D6  (3D View)
Global Stoichiometry: Hetero 24-mer - A12B12 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 887.6 kDa 
• Atom Count: 60,180 
• Modelled Residue Count: 7,644 
• Deposited Residue Count: 7,920 
• Unique protein chains: 2

 8FWJ

Structure of dodecameric KaiC-RS-S413E/S414E complexed with KaiB-RS solved by cryo-EM

• PDB DOI:  https://doi.org/10.2210/pdb8FWJ/pdb
• EM Map EMD-29506: EMDB EMDataResource

• Classification: CIRCADIAN CLOCK PROTEIN
• Organism(s): Cereibacter sphaeroides
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-01-22 Released: 2023-03-22 
• Deposition Author(s): Padua, R.A.P., Grant, T., Pitsawong, W., Hoemberger, M.S., Otten, R., Bradshaw, N., Grigorieff, N., Kern, D.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

From primordial clocks to circadian oscillators.

Pitsawong, W., Padua, R.A.P., Grant, T., Hoemberger, M., Otten, R., Bradshaw, N., Grigorieff, N., Kern, D.

(2023) Nature 616: 183-189

• PubMed: 36949197 
• DOI: https://doi.org/10.1038/s41586-023-05836-9
• Primary Citation of Related Structures:  
  8DB3, 8DBA, 8FWI, 8FWJ


• PubMed Abstract: 
  

Circadian rhythms play an essential part in many biological processes, and only three prokaryotic proteins are required to constitute a true post-translational circadian oscillator ¹ . The evolutionary history of the three Kai proteins indicates that KaiC is the oldest member and a central component of the clock ² . Subsequent additions of KaiB and KaiA regulate the phosphorylation state of KaiC for time synchronization. The canonical KaiABC system in cyanobacteria is well understood ^3-6 , but little is known about more ancient systems that only possess KaiBC. However, there are reports that they might exhibit a basic, hourglass-like timekeeping mechanism ^7-9 . Here we investigate the primordial circadian clock in Rhodobacter sphaeroides, which contains only KaiBC, to elucidate its inner workings despite missing KaiA. Using a combination of X-ray crystallography and cryogenic electron microscopy, we find a new dodecameric fold for KaiC, in which two hexamers are held together by a coiled-coil bundle of 12 helices. This interaction is formed by the carboxy-terminal extension of KaiC and serves as an ancient regulatory moiety that is later superseded by KaiA. A coiled-coil register shift between daytime and night-time conformations is connected to phosphorylation sites through a long-range allosteric network that spans over 140 Å. Our kinetic data identify the difference in the ATP-to-ADP ratio between day and night as the environmental cue that drives the clock. They also unravel mechanistic details that shed light on the evolution of self-sustained oscillators.

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Organizational Affiliation: 

Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Circadian clock protein KaiC	A, B, C, D, E, F, G, H, I, J, K, L	568	Cereibacter sphaeroides	Mutation(s): 2
UniProt
Find proteins for B9KWX8 (Cereibacter sphaeroides (strain KD131 / KCTC 12085)) Explore B9KWX8  Go to UniProtKB:  B9KWX8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Circadian clock protein KaiB	M, N, O, P, Q, R, S, T, U, V, W, X	92	Cereibacter sphaeroides	Mutation(s): 0  Gene Names: EBL86_22425
UniProt
Find proteins for A0A3G6WWB7 (Cereibacter sphaeroides) Explore A0A3G6WWB7  Go to UniProtKB:  A0A3G6WWB7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	AB [auth H], DA [auth B], EB [auth I], HA [auth C], IB [auth J], LA [auth D], MB [auth K], PA [auth E], QB [auth L], TA [auth F], WA [auth G], Y [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP	BB [auth H], EA [auth B], FB [auth I], IA [auth C], JB [auth J], MA [auth D], NB [auth K], QA [auth E], RB [auth L], UA [auth F], XA [auth G], Z [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	AA [auth A], BA [auth A], CA [auth A], CB [auth H], DB [auth H], FA [auth B], GA [auth B], GB [auth I], HB [auth I], JA [auth C], KA [auth C], KB [auth J], LB [auth J], NA [auth D], OA [auth D], OB [auth K], PB [auth K], RA [auth E], SA [auth E], SB [auth L], TB [auth L], VA [auth F], YA [auth G], ZA [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cisTEM	2.0.0-alpha
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-22 
Deposition Author(s): Padua, R.A.P., Grant, T., Pitsawong, W., Hoemberger, M.S., Otten, R., Bradshaw, N., Grigorieff, N., Kern, D.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2023-03-22
  Type: Initial release
  
• Version 1.1: 2023-04-05
  Changes: Database references
• Version 1.2: 2023-04-19
  Changes: Database references