6PTZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

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Ligand Structure Quality Assessment 


This is version 1.4 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 U S A 116: 19449-19457

  • DOI: https://doi.org/10.1073/pnas.1907875116
  • Primary Citation of Related Structures:  
    6PTZ, 6PU0

  • 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 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

    Department of Chemistry, Southern Methodist University, Dallas, TX 75275.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cryptochrome-1502Columba liviaMutation(s): 1 
Gene Names: A306_00007326
UniProt
Find proteins for A0A2I0LZR8 (Columba livia)
Explore A0A2I0LZR8 
Go to UniProtKB:  A0A2I0LZR8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2I0LZR8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
K [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.733α = 90
b = 85.574β = 90
c = 103.283γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB-1613643
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS095899
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesDA042072
European Research Council (ERC)European Union340451
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM090247
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM112991
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM127122
German Research Foundation (DFG)GermanySFB 1372
German Research Foundation (DFG)GermanyGRK 1885
Other governmentUnited StatesFA9550-14-1-0095

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-09
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description