High resolution structure of mouse Cryptochrome 1

Experimental Data Snapshot

  • Resolution: 1.84 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 

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This is version 1.5 of the entry. See complete history


Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1.

Michael, A.K.Fribourgh, J.L.Chelliah, Y.Sandate, C.R.Hura, G.L.Schneidman-Duhovny, D.Tripathi, S.M.Takahashi, J.S.Partch, C.L.

(2017) Proc Natl Acad Sci U S A 114: 1560-1565

  • DOI: https://doi.org/10.1073/pnas.1615310114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The basic helix-loop-helix PAS domain (bHLH-PAS) transcription factor CLOCK:BMAL1 (brain and muscle Arnt-like protein 1) sits at the core of the mammalian circadian transcription/translation feedback loop. Precise control of CLOCK:BMAL1 activity by coactivators and repressors establishes the ∼24-h periodicity of gene expression. Formation of a repressive complex, defined by the core clock proteins cryptochrome 1 (CRY1):CLOCK:BMAL1, plays an important role controlling the switch from repression to activation each day. Here we show that CRY1 binds directly to the PAS domain core of CLOCK:BMAL1, driven primarily by interaction with the CLOCK PAS-B domain. Integrative modeling and solution X-ray scattering studies unambiguously position a key loop of the CLOCK PAS-B domain in the secondary pocket of CRY1, analogous to the antenna chromophore-binding pocket of photolyase. CRY1 docks onto the transcription factor alongside the PAS domains, extending above the DNA-binding bHLH domain. Single point mutations at the interface on either CRY1 or CLOCK disrupt formation of the ternary complex, highlighting the importance of this interface for direct regulation of CLOCK:BMAL1 activity by CRY1.

  • Organizational Affiliation

    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cryptochrome-1491Mus musculusMutation(s): 0 
Gene Names: Cry1
UniProt & NIH Common Fund Data Resources
Find proteins for P97784 (Mus musculus)
Explore P97784 
Go to UniProtKB:  P97784
IMPC:  MGI:1270841
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP97784
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CL

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.84 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.63α = 71.62
b = 51.035β = 84.12
c = 54.175γ = 88.89
Software Package:
Software NamePurpose
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM107069
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA189660

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2017-02-15
    Changes: Database references
  • Version 1.2: 2017-02-22
    Changes: Database references
  • Version 1.3: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Refinement description