Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 59.22 kDa 
• Atom Count: 4126 
• Modelled Residue Count: 485 
• Deposited Residue Count: 509 
• Unique protein chains: 1

1U3D

Crystal Structure of the PHR domain of Cryptochrome 1 from Arabidopsis thaliana with AMPPNP bound

• DOI: 10.2210/pdb1U3D/pdb

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


• Deposited: 2004-07-21 Released: 2004-08-24 
• Deposition Author(s): Brautigam, C.A., Smith, B.S., Ma, Z., Palnitkar, M., Tomchick, D.R., Machius, M., Deisenhofer, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.253 
• R-Value Work: 0.204 
• R-Value Observed: 0.204 

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

• PubMed: 15299148 
• DOI: 10.1073/pnas.0404851101
• Primary Citation of Related Structures:  
  1U3D, 1U3C


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cryptochrome 1 apoprotein	A	509	Arabidopsis thaliana	Mutation(s): 0  Gene Names: CRY1, BLU1, HY4, At4g08920, T3H13.14, T3H13.5
UniProt
Find proteins for Q43125 (Arabidopsis thaliana) Explore Q43125  Go to UniProtKB:  Q43125

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	G [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
ANP (Subject of Investigation/LOI)	H [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
NDS (Subject of Investigation/LOI)	I [auth A]	ETHYL DIMETHYL AMMONIO PROPANE SULFONATE C7 H17 N O3 S NNCRHRDBFDCWPA-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A], C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ANP	Binding MOAD:  1U3D	Kd: 7.50e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.253 
• R-Value Work: 0.204 
• R-Value Observed: 0.204 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.213	α = 90
b = 169.213	β = 90
c = 104.521	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2004-07-21 
• Released Date: 2004-08-24 
Deposition Author(s): Brautigam, C.A., Smith, B.S., Ma, Z., Palnitkar, M., Tomchick, D.R., Machius, M., Deisenhofer, J.

Revision History  

• 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