5VJI

Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of the CLOCK Transactivation Domain Exon19 in Complex with a Repressor.

Hou, Z.Su, L.Pei, J.Grishin, N.V.Zhang, H.

(2017) Structure 25: 1187-1194.e3

  • DOI: 10.1016/j.str.2017.05.023
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In the canonical clock model, CLOCK:BMAL1-mediated transcriptional activation is feedback regulated by its repressors CRY and PER and, in association with other coregulators, ultimately generates oscillatory gene expression patterns. How CLOCK:BMAL1 ...

    In the canonical clock model, CLOCK:BMAL1-mediated transcriptional activation is feedback regulated by its repressors CRY and PER and, in association with other coregulators, ultimately generates oscillatory gene expression patterns. How CLOCK:BMAL1 interacts with coregulator(s) is not well understood. Here we report the crystal structures of the mouse CLOCK transactivating domain Exon19 in complex with CIPC, a potent circadian repressor that functions independently of CRY and PER. The Exon19:CIPC complex adopts a three-helical coiled-coil bundle conformation containing two Exon19 helices and one CIPC. Unique to Exon19:CIPC, three highly conserved polar residues, Asn341 of CIPC and Gln544 of the two Exon19 helices, are located at the mid-section of the coiled-coil bundle interior and form hydrogen bonds with each other. Combining results from protein database search, sequence analysis, and mutagenesis studies, we discovered for the first time that CLOCK Exon19:CIPC interaction is a conserved transcription regulatory mechanism among mammals, fish, flies, and other invertebrates.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Circadian locomoter output cycles protein kaput
A, B, D, E
51Mus musculusMutation(s): 0 
Gene Names: Clock
EC: 2.3.1.48
Find proteins for O08785 (Mus musculus)
Go to UniProtKB:  O08785
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CLOCK-interacting pacemaker
C, F
64Mus musculusMutation(s): 0 
Gene Names: Cipc (Kiaa1737)
Find proteins for Q8R0W1 (Mus musculus)
Go to UniProtKB:  Q8R0W1
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 24.339α = 90.00
b = 77.585β = 90.00
c = 150.363γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM104496
Welch FoundationUnited StatesI1505

Revision History 

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-07-19
    Type: Database references
  • Version 1.2: 2017-08-16
    Type: Database references
  • Version 1.3: 2017-09-06
    Type: Author supporting evidence