9DC0 | pdb_00009dc0

Crystal Structure of European Robin CRY1

• PDB DOI: https://doi.org/10.2210/pdb9DC0/pdb

• Classification: CIRCADIAN CLOCK PROTEIN
• Organism(s): Erithacus rubecula
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2024-08-24 Released: 2025-08-27 
• Deposition Author(s): Wickramaratne, A., Chelliah, Y., Green, C.B., Takahashi, J.S., Zoltowski, B.D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.274 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Structure of European robin cryptochrome 1 reveals a role in circadian rhythms, not magnetoreception.

Wickramaratne, A.C., Rasmussen, E.S., Chelliah, Y., Schuhmann, F., Solov'yov, I.A., Mouritsen, H., Green, C.B., Zoltowski, B.D., Takahashi, J.S.

(2025) iScience 28: 114015-114015

• PubMed: 41488359 
• DOI: https://doi.org/10.1016/j.isci.2025.114015
• Primary Citation Related Structures: 
  9DC0


• PubMed Abstract: 
  

  Cryptochromes (CRYs) play critical roles in regulating diverse physiological functions, including circadian rhythms and neuronal firing in light-dependent or -independent fashions. Structural studies of CRYs have highlighted common features, such as the photolyase homology region (PHR), but they also reveal key differences, particularly in the binding of the flavin adenine dinucleotide (FAD) cofactor, leading to a long-standing debate, namely, whether Type I CRYs can function as FAD-dependent photosensors. This study solves the first crystal structure of a Type II CRY from a migratory songbird, namely, the European robin ( Erithacus rubecula ) CRY1. Structural, biochemical, and computational analyses of erCRY1 reveal that, unlike light-activated Type I and IV CRYs, Type II CRYs do not bind FAD and employ an open primary pocket for protein-protein interactions. These findings offer new insights into the structural basis of CRY function and suggest that migratory song-bird Type II CRYs function as circadian regulators, not magnetoreceptors.

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Organizational Affiliation: 
• Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA.
Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark.
Institute of Physics, Carl von Ossietzky Universität Oldenburg, Carl-von-Ossietzky Str. 9-11, 26129 Oldenburg, Germany.
Research Centre for Neurosensory Science, Carl von Ossietzky Universität Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany.
Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg, Ammerländer Heerstr. 114-118, 26129 Oldenburg, Germany.
AG Neurosensory Sciences/Animal Navigation, Institut für Biologie und Umweltwissenschaften, Carl-von-Ossietzky Universität Oldenburg, Oldenburg, Germany.
Department of Chemistry, Southern Methodist University, Dallas, TX 75275, USA.
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 59.09 kDa 
• Atom Count: 4,167 
• Modeled Residue Count: 488 
• Deposited Residue Count: 515 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cryptochrome-1	A	515	Erithacus rubecula	Mutation(s): 0  Gene Names: CRY1b
UniProt
Find proteins for A0A7K7GUF1 (Erithacus rubecula) Explore A0A7K7GUF1  Go to UniProtKB:  A0A7K7GUF1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.274 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.115	α = 90
b = 79.602	β = 90
c = 127.986	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-27 
Deposition Author(s): Wickramaratne, A., Chelliah, Y., Green, C.B., Takahashi, J.S., Zoltowski, B.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	2R15GM109282
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM127122
Howard Hughes Medical Institute (HHMI)	United States	Investigator Award

Revision History  

• Version 1.0: 2025-08-27
  Type: Initial release
  
• Version 1.1: 2026-03-18
  Changes: Database references