5VJI | pdb_00005vji

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 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5VJI

This is version 1.5 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: https://doi.org/10.1016/j.str.2017.05.023
  • Primary Citation Related Structures: 
    5VJI, 5VJX

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 39.2 kDa 
  • Atom Count: 2,562 
  • Modeled Residue Count: 296 
  • Deposited Residue Count: 332 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Circadian locomoter output cycles protein kaput
A, B, D, E
51Mus musculusMutation(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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO08785
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
CLOCK-interacting pacemaker
C, F
64Mus musculusMutation(s): 0 
Gene Names: CipcKiaa1737
UniProt
Find proteins for Q8R0W1 (Mus musculus)
Explore Q8R0W1 
Go to UniProtKB:  Q8R0W1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8R0W1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, D, E
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 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 24.339α = 90
b = 77.585β = 90
c = 150.363γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM104496
Welch FoundationUnited StatesI1505

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-07-19
    Changes: Database references
  • Version 1.2: 2017-08-16
    Changes: Database references
  • Version 1.3: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.4: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.5: 2024-11-06
    Changes: Data collection, Database references, Structure summary