2J4D

Cryptochrome 3 from Arabidopsis thaliana

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Cryptochrome 3 from Arabidopsis Thaliana: Structural and Functional Analysis of its Complex with a Folate Light Antenna

Klar, T., Pokorny, R., Moldt, J., Batschauer, A., Essen, L.-O.

(2007) J Mol Biol 366: 954

  • DOI: 10.1016/j.jmb.2006.11.066
  • Primary Citation of Related Structures:  
    2J4D

  • PubMed Abstract: 

    • Cryptochromes are almost ubiquitous blue-light receptors and act in several species as central components of the circadian clock. Despite being evolutionary and structurally related with DNA photolyases, a class of light-driven DNA-repair enzymes, and ha ...

    Cryptochromes are almost ubiquitous blue-light receptors and act in several species as central components of the circadian clock. Despite being evolutionary and structurally related with DNA photolyases, a class of light-driven DNA-repair enzymes, and having similar cofactor compositions, cryptochromes lack DNA-repair activity. Cryptochrome 3 from the plant Arabidopsis thaliana belongs to the DASH-type subfamily. Its crystal structure determined at 1.9 Angstroms resolution shows cryptochrome 3 in a dimeric state with the antenna cofactor 5,10-methenyltetrahydrofolate (MTHF) bound in a distance of 15.2 Angstroms to the U-shaped FAD chromophore. Spectroscopic studies on a mutant where a residue crucial for MTHF-binding, E149, was replaced by site-directed mutagenesis demonstrate that MTHF acts in cryptochrome 3 as a functional antenna for the photoreduction of FAD.

    Related Citations: 
    • Crystallization and Preliminary X-Ray Analysis of Cryptochrome 3 from Arabidopsis Thaliana
      Pokorny, R., Klar, T., Essen, L.-O., Batschauer, A.
      (2005) Acta Crystallogr Sect F Struct Biol Cryst Commun 61: 935
    Organizational Affiliation: 

    Philipps-Universität Marburg, Department of Chemistry, Hans-Meerwein-Strasse, D-35032 Marburg, Germany.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CRYPTOCHROME DASH A, B525Arabidopsis thalianaMutation(s): 0 
Gene Names: CRYD, CRY3, At5g24850, F6A4.60
Find proteins for Q84KJ5 (Arabidopsis thaliana)
Explore Q84KJ5 
Go to UniProtKB:  Q84KJ5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
Download Ideal Coordinates CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
MHF
Query on MHF
Download Ideal Coordinates CCD File 
A, B
5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID
C20 H23 N7 O6
QYNUQALWYRSVHF-OLZOCXBDSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.298α = 90
b = 116.782β = 90
c = 135.024γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Advisory, Data collection