Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C6  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 173.83 kDa 
• Atom Count: 12055 
• Residue Count: 1346 
• Unique protein chains: 1

4TLB

Crystal structure of N-terminal C1 domain of KaiC

• DOI: 10.2210/pdb4TLB/pdb

• Classification: TRANSFERASE
• Organism(s): Synechococcus elongatus PCC 7942 = FACHB-805
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-05-29 Released: 2015-07-01 
• Deposition Author(s): Abe, J., Hiyama, T.B., Mukaiyama, A., Son, S., Akiyama, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.199 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

Literature

Circadian rhythms. Atomic-scale origins of slowness in the cyanobacterial circadian clock.

Abe, J., Hiyama, T.B., Mukaiyama, A., Son, S., Mori, T., Saito, S., Osako, M., Wolanin, J., Yamashita, E., Kondo, T., Akiyama, S.

(2015) Science 349: 312-316

• PubMed: 26113637 
• DOI: 10.1126/science.1261040
• Primary Citation of Related Structures:  
  4TLD, 4TLE, 4TLA, 4TLB, 4TLC, 4TL6, 4TL7, 4TL8, 4TL9


• PubMed Abstract: 
  

Circadian clocks generate slow and ordered cellular dynamics but consist of fast-moving bio-macromolecules; consequently, the origins of the overall slowness remain unclear. We identified the adenosine triphosphate (ATP) catalytic region [adenosine triphosphatase (ATPase)] in the amino-terminal half of the clock protein KaiC as the minimal pacemaker that controls the in vivo frequency of the cyanobacterial clock. Crystal structures of the ATPase revealed that the slowness of this ATPase arises from sequestration of a lytic water molecule in an unfavorable position and coupling of ATP hydrolysis to a peptide isomerization with high activation energy. The slow ATPase is coupled with another ATPase catalyzing autodephosphorylation in the carboxyl-terminal half of KaiC, yielding the circadian response frequency of intermolecular interactions with other clock-related proteins that influences the transcription and translation cycle.

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Organizational Affiliation: 

Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan. Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Circadian clock protein kinase KaiC	A, B, C, D, E, F	253	Synechococcus elongatus PCC 7942 = FACHB-805	Mutation(s): 1  Gene Names: kaiC, Synpcc7942_1216, see0011 EC: 2.7.11.1
Find proteins for Q79PF4 (Synechococcus elongatus (strain PCC 7942 / FACHB-805)) Explore Q79PF4  Go to UniProtKB:  Q79PF4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGS	A, B, C, D, E, F	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C10 H16 N5 O12 P3 S NLTUCYMLOPLUHL-KQYNXXCUSA-N
CL	A, B, C, D, E, F	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	A, B, C, D, E, F	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.199 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.06	α = 90
b = 133.562	β = 90
c = 150.835	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-05-29 
• Released Date: 2015-07-01 
Deposition Author(s): Abe, J., Hiyama, T.B., Mukaiyama, A., Son, S., Akiyama, S.

Revision History 

• Version 1.0: 2015-07-01
  Type: Initial release
  
• Version 1.1: 2015-08-05
  Changes: Database references
• Version 1.2: 2020-01-29
  Changes: Data collection, Database references, Derived calculations