6PU0 | pdb_00006pu0

Pigeon Cryptochrome4 bound to flavin adenine dinucleotide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.195 (Depositor), 0.196 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 
    0.160 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6PU0

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 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.

Macromolecule Content 

  • Total Structure Weight: 59.7 kDa 
  • Atom Count: 4,372 
  • Modeled Residue Count: 480 
  • Deposited Residue Count: 502 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cryptochrome-1502Columba liviaMutation(s): 0 
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
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
(Subject of Investigation/LOI)

Query on FAD



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

Query on PGE



Download:Ideal Coordinates CCD File
C [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



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

Query on GOL



Download:Ideal Coordinates CCD File
I [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
D [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.195 (Depositor), 0.196 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 0.160 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.099α = 90
b = 86.578β = 90
c = 104.267γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



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
Air Force Office of Scientific ResearchUnited 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