8DD7

The Cryo-EM structure of Drosophila Cryptochrome in complex with Timeless


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Cryptochrome-Timeless structure reveals circadian clock timing mechanisms.

Lin, C.Feng, S.DeOliveira, C.C.Crane, B.R.

(2023) Nature 617: 194-199

  • DOI: https://doi.org/10.1038/s41586-023-06009-4
  • Primary Citation of Related Structures:  
    8DD7

  • PubMed Abstract: 

    Circadian rhythms influence many behaviours and diseases 1,2 . They arise from oscillations in gene expression caused by repressor proteins that directly inhibit transcription of their own genes. The fly circadian clock offers a valuable model for studying these processes, wherein Timeless (Tim) plays a critical role in mediating nuclear entry of the transcriptional repressor Period (Per) and the photoreceptor Cryptochrome (Cry) entrains the clock by triggering Tim degradation in light 2,3 . Here, through cryogenic electron microscopy of the Cry-Tim complex, we show how a light-sensing cryptochrome recognizes its target. Cry engages a continuous core of amino-terminal Tim armadillo repeats, resembling how photolyases recognize damaged DNA, and binds a C-terminal Tim helix, reminiscent of the interactions between light-insensitive cryptochromes and their partners in mammals. The structure highlights how the Cry flavin cofactor undergoes conformational changes that couple to large-scale rearrangements at the molecular interface, and how a phosphorylated segment in Tim may impact clock period by regulating the binding of Importin-α and the nuclear import of Tim-Per 4,5 . Moreover, the structure reveals that the N terminus of Tim inserts into the restructured Cry pocket to replace the autoinhibitory C-terminal tail released by light, thereby providing a possible explanation for how the long-short Tim polymorphism adapts flies to different climates 6,7 .


  • Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methylated-DNA--protein-cysteine methyltransferase,Cryptochrome-1 fusion746Homo sapiensDrosophila melanogaster
This entity is chimeric
Mutation(s): 0 
UniProt
Find proteins for E5BBQ0 (Homo sapiens)
Explore E5BBQ0 
Go to UniProtKB:  E5BBQ0
Find proteins for O77059 (Drosophila melanogaster)
Explore O77059 
Go to UniProtKB:  O77059
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsE5BBQ0O77059
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein timeless,Methylated-DNA--protein-cysteine methyltransferase fusion1,618Drosophila melanogasterHomo sapiens
This entity is chimeric
Mutation(s): 0 
EC: 2.1.1.63
UniProt
Find proteins for P49021 (Drosophila melanogaster)
Explore P49021 
Go to UniProtKB:  P49021
Find proteins for E5BBQ0 (Homo sapiens)
Explore E5BBQ0 
Go to UniProtKB:  E5BBQ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsE5BBQ0P49021
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM122535

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release
  • Version 1.1: 2023-04-26
    Changes: Database references
  • Version 1.2: 2023-05-10
    Changes: Database references
  • Version 1.3: 2023-05-17
    Changes: Database references