4H10

Intermolecular recognition revealed by the complex structure of human CLOCK-BMAL1 basic Helix-Loop-Helix domains with E-box DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.402 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Intermolecular recognition revealed by the complex structure of human CLOCK-BMAL1 basic helix-loop-helix domains with E-box DNA.

Wang, Z.Wu, Y.Li, L.Su, X.D.

(2013) Cell Res. 23: 213-224

  • DOI: 10.1038/cr.2012.170

  • PubMed Abstract: 
  • CLOCK (circadian locomotor output cycles kaput) and BMAL1 (brain and muscle ARNT-like 1) are both transcription factors of the circadian core loop in mammals. Recently published mouse CLOCK-BMAL1 bHLH (basic helix-loop-helix)-PAS (period-ARNT-single- ...

    CLOCK (circadian locomotor output cycles kaput) and BMAL1 (brain and muscle ARNT-like 1) are both transcription factors of the circadian core loop in mammals. Recently published mouse CLOCK-BMAL1 bHLH (basic helix-loop-helix)-PAS (period-ARNT-single-minded) complex structure sheds light on the mechanism for heterodimer formation, but the structural details of the protein-DNA recognition mechanisms remain elusive. Here we have elucidated the crystal structure of human CLOCK-BMAL1 bHLH domains bound to a canonical E-box DNA. We demonstrate that CLOCK and BMAL1 bHLH domains can be mutually selected, and that hydrogen-bonding networks mediate their E-box recognition. We identified a hydrophobic contact between BMAL1 Ile80 and a flanking thymine nucleotide, suggesting that CLOCK-BMAL1 actually reads 7-bp DNA and not the previously believed 6-bp DNA. To find potential non-canonical E-boxes that could be recognized by CLOCK-BMAL1, we constructed systematic single-nucleotide mutations on the E-box and measured their relevant affinities. We defined two non-canonical E-box patterns with high affinities, AACGTGA and CATGTGA, in which the flanking A7-T7' base pair is indispensable for recognition. These results will help us to identify functional CLOCK-BMAL1-binding sites in vivo and to search for clock-controlled genes. Furthermore, we assessed the inhibitory role of potential phosphorylation sites in bHLH regions. We found that the phospho-mimicking mutation on BMAL1 Ser78 could efficiently block DNA binding as well as abolish normal circadian oscillation in cells. We propose that BMAL1 Ser78 should be a key residue mediating input signal-regulated transcriptional inhibition for external cues to entrain the circadian clock by kinase cascade.


    Organizational Affiliation

    State Key Laboratory of Protein and Plant Gene Research, and Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aryl hydrocarbon receptor nuclear translocator-like protein 1
A
73Homo sapiensMutation(s): 0 
Gene Names: ARNTL (BHLHE5, BMAL1, MOP3, PASD3)
Find proteins for O00327 (Homo sapiens)
Go to Gene View: ARNTL
Go to UniProtKB:  O00327
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Circadian locomoter output cycles protein kaput
B
71Homo sapiensMutation(s): 0 
Gene Names: CLOCK (BHLHE8, KIAA0334)
EC: 2.3.1.48
Find proteins for O15516 (Homo sapiens)
Go to Gene View: CLOCK
Go to UniProtKB:  O15516
Entity ID: 3
MoleculeChainsLengthOrganism
E-box DNA sense strandC15N/A
Entity ID: 4
MoleculeChainsLengthOrganism
E-box DNA antisense strandD15N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.402 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.195 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 98.740α = 90.00
b = 98.740β = 90.00
c = 62.880γ = 120.00
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-09-10 
  • Released Date: 2012-12-26 
  • Deposition Author(s): Wang, Z., Su, X.-D.

Revision History 

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-02-20
    Type: Database references