2J4D | pdb_00002j4d

Cryptochrome 3 from Arabidopsis thaliana

• PDB DOI: https://doi.org/10.2210/pdb2J4D/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-08-28 Released: 2007-06-19 
• Deposition Author(s): Klar, T., Pokorny, R., Batschauer, A., Essen, L.-O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

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 Biology 366: 954

• PubMed: 17188299 
• DOI: https://doi.org/10.1016/j.jmb.2006.11.066
• Primary Citation 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 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.

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Organizational Affiliation: 
• Philipps-Universität Marburg, Department of Chemistry, Hans-Meerwein-Strasse, D-35032 Marburg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 123.15 kDa 
• Atom Count: 9,038 
• Modeled Residue Count: 995 
• Deposited Residue Count: 1,050 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRYPTOCHROME DASH	A, B	525	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q84KJ5 (Arabidopsis thaliana) Explore Q84KJ5  Go to UniProtKB:  Q84KJ5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], E [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
MHF	D [auth A], F [auth B]	5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID C20 H23 N7 O6 QYNUQALWYRSVHF-OLZOCXBDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.298	α = 90
b = 116.782	β = 90
c = 135.024	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-19 
Deposition Author(s): Klar, T., Pokorny, R., Batschauer, A., Essen, L.-O.

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
• Version 1.4: 2023-12-13
  Changes: Advisory, Data collection, Database references, Other, Refinement description