2J4D

Cryptochrome 3 from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
  • Also Cited By: 2VTB

  • 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, an ...

    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 61: 935


    Organizational Affiliation

    Philipps-Universit├Ąt Marburg, Department of Chemistry, Hans-Meerwein-Strasse, D-35032 Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRYPTOCHROME DASH
A, B
525Arabidopsis thalianaMutation(s): 0 
Gene Names: CRYD (CRY3)
Find proteins for Q84KJ5 (Arabidopsis thaliana)
Go to UniProtKB:  Q84KJ5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MHF
Query on MHF

Download SDF File 
Download CCD File 
A, B
5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID
C20 H23 N7 O6
QYNUQALWYRSVHF-OLZOCXBDSA-N
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 76.298α = 90.00
b = 116.782β = 90.00
c = 135.024γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance