4F3L

Crystal Structure of the Heterodimeric CLOCK:BMAL1 Transcriptional Activator Complex

• PDB DOI:  https://doi.org/10.2210/pdb4F3L/pdb

• Classification: TRANSCRIPTION/ACTIVATOR
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2012-05-09 Released: 2012-06-06 
• Deposition Author(s): Huang, N., Chelliah, Y., Shan, Y., Taylor, C., Yoo, S., Partch, C., Green, C.B., Zhang, H., Takahashi, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.217 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

Crystal structure of the heterodimeric CLOCK:BMAL1 transcriptional activator complex.

Huang, N., Chelliah, Y., Shan, Y., Taylor, C.A., Yoo, S.H., Partch, C., Green, C.B., Zhang, H., Takahashi, J.S.

(2012) Science 337: 189-194

• PubMed: 22653727 
• DOI: https://doi.org/10.1126/science.1222804
• Primary Citation of Related Structures:  
  4F3L


• PubMed Abstract: 
  

The circadian clock in mammals is driven by an autoregulatory transcriptional feedback mechanism that takes approximately 24 hours to complete. A key component of this mechanism is a heterodimeric transcriptional activator consisting of two basic helix-loop-helix PER-ARNT-SIM (bHLH-PAS) domain protein subunits, CLOCK and BMAL1. Here, we report the crystal structure of a complex containing the mouse CLOCK:BMAL1 bHLH-PAS domains at 2.3 Å resolution. The structure reveals an unusual asymmetric heterodimer with the three domains in each of the two subunits--bHLH, PAS-A, and PAS-B--tightly intertwined and involved in dimerization interactions, resulting in three distinct protein interfaces. Mutations that perturb the observed heterodimer interfaces affect the stability and activity of the CLOCK:BMAL1 complex as well as the periodicity of the circadian oscillator. The structure of the CLOCK:BMAL1 complex is a starting point for understanding at an atomic level the mechanism driving the mammalian circadian clock.

---

Organizational Affiliation: 

Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 86.28 kDa 
• Atom Count: 5,278 
• Modelled Residue Count: 621 
• Deposited Residue Count: 748 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BMAL1b	A [auth B]	387	Mus musculus	Mutation(s): 0  Gene Names: Arntl, Bmal1, bmal1b
UniProt
Find proteins for Q9WTL8 (Mus musculus) Explore Q9WTL8  Go to UniProtKB:  Q9WTL8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Circadian locomoter output cycles protein kaput	B [auth A]	361	Mus musculus	Mutation(s): 0  Gene Names: Clock EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for O08785 (Mus musculus) Explore O08785  Go to UniProtKB:  O08785
IMPC:  MGI:99698

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.217 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.242	α = 90
b = 71.955	β = 90
c = 173.306	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
SHARP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-06 
Deposition Author(s): Huang, N., Chelliah, Y., Shan, Y., Taylor, C., Yoo, S., Partch, C., Green, C.B., Zhang, H., Takahashi, J.

Revision History  

• Version 1.0: 2012-06-06
  Type: Initial release
  
• Version 1.1: 2012-08-01
  Changes: Database references
• Version 1.2: 2018-12-05
  Changes: Data collection