6PTZ

Crystal structure of pigeon Cryptochrome 4 mutant Y319D in complex with flavin adenine dinucleotide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.793 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Chemical and structural analysis of a photoactive vertebrate cryptochrome from pigeon.

Zoltowski, B.D.Chelliah, Y.Wickramaratne, A.Jarocha, L.Karki, N.Xu, W.Mouritsen, H.Hore, P.J.Hibbs, R.E.Green, C.B.Takahashi, J.S.

(2019) Proc.Natl.Acad.Sci.USA 116: 19449-19457

  • DOI: 10.1073/pnas.1907875116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Computational and biochemical studies implicate the blue-light sensor cryptochrome (CRY) as an endogenous light-dependent magnetosensor enabling migratory birds to navigate using the Earth's magnetic field. Validation of such a mechanism has been ham ...

    Computational and biochemical studies implicate the blue-light sensor cryptochrome (CRY) as an endogenous light-dependent magnetosensor enabling migratory birds to navigate using the Earth's magnetic field. Validation of such a mechanism has been hampered by the absence of structures of vertebrate CRYs that have functional photochemistry. Here we present crystal structures of Columba livia (pigeon) CRY4 that reveal evolutionarily conserved modifications to a sequence of Trp residues (Trp-triad) required for CRY photoreduction. In Cl CRY4, the Trp-triad chain is extended to include a fourth Trp (W369) and a Tyr (Y319) residue at the protein surface that imparts an unusually high quantum yield of photoreduction. These results are consistent with observations of night migratory behavior in animals at low light levels and could have implications for photochemical pathways allowing magnetosensing.


    Organizational Affiliation

    Center for Drug Discovery, Design, and Delivery, Southern Methodist University, Dallas, TX 75275.,Research Center for Neurosensory Sciences, University of Oldenburg, DE-26111 Oldenburg, Germany.,Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390; joseph.takahashi@utsouthwestern.edu.,Department of Chemistry, University of Oxford, OX1 3QZ Oxford, United Kingdom.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390.,Institute for Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, DE-26111 Oldenburg, Germany.,Department of Chemistry, Southern Methodist University, Dallas, TX 75275.,Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cryptochrome-1
A
502Columba liviaMutation(s): 1 
Find proteins for A0A2I0LZR8 (Columba livia)
Go to UniProtKB:  A0A2I0LZR8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.793 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.733α = 90.00
b = 85.574β = 90.00
c = 103.283γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United StatesMCB-1613643
National Institutes of Health/National Institute of Neurological Disorders and StrokeUnited StatesNS095899
National Institutes of Health/National Institute on Drug AbuseUnited StatesDA042072
European Research Council340451
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM090247
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM112991
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR35 GM127122
German Research FoundationGermanySFB 1372
German Research FoundationGermanyGRK 1885
Other governmentUnited StatesFA9550-14-1-0095

Revision History 

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-09-18
    Type: Data collection, Database references
  • Version 1.2: 2019-10-09
    Type: Data collection, Database references