1U3C

Crystal Structure of the PHR domain of Cryptochrome 1 from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.254 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FADClick on this verticalbar to view detailsBest fitted NDSClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Structure of the photolyase-like domain of cryptochrome 1 from Arabidopsis thaliana.

Brautigam, C.A.Smith, B.S.Ma, Z.Palnitkar, M.Tomchick, D.R.Machius, M.Deisenhofer, J.

(2004) Proc Natl Acad Sci U S A 101: 12142-12147

  • DOI: https://doi.org/10.1073/pnas.0404851101
  • Primary Citation of Related Structures:  
    1U3C, 1U3D

  • PubMed Abstract: 

    Signals generated by cryptochrome (CRY) blue-light photoreceptors are responsible for a variety of developmental and circadian responses in plants. The CRYs are also identified as circadian blue-light photoreceptors in Drosophila and components of the mammalian circadian clock. These flavoproteins all have an N-terminal domain that is similar to photolyase, and most have an additional C-terminal domain of variable length. We present here the crystal structure of the photolyase-like domain of CRY-1 from Arabidopsis thaliana. The structure reveals a fold that is very similar to photolyase, with a single molecule of FAD noncovalently bound to the protein. The surface features of the protein and the dissimilarity of a surface cavity to that of photolyase account for its lack of DNA-repair activity. Previous in vitro experiments established that the photolyase-like domain of CRY-1 can bind Mg.ATP, and we observe a single molecule of an ATP analog bound in the aforementioned surface cavity, near the bound FAD cofactor. The structure has implications for the signaling mechanism of CRY blue-light photoreceptors.


  • Organizational Affiliation

    Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9050, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cryptochrome 1 apoprotein509Arabidopsis thalianaMutation(s): 0 
Gene Names: CRY1
UniProt
Find proteins for Q43125 (Arabidopsis thaliana)
Explore Q43125 
Go to UniProtKB:  Q43125
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ43125
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
F [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
NDS
Query on NDS

Download Ideal Coordinates CCD File 
G [auth A]ETHYL DIMETHYL AMMONIO PROPANE SULFONATE
C7 H17 N O3 S
NNCRHRDBFDCWPA-UHFFFAOYSA-N
HEZ
Query on HEZ

Download Ideal Coordinates CCD File 
H [auth A]HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
CL
Query on CL

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E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.254 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.43α = 90
b = 169.43β = 90
c = 104.245γ = 120
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FADClick on this verticalbar to view detailsBest fitted NDSClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-24
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary