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- PDB-8dd7: The Cryo-EM structure of Drosophila Cryptochrome in complex with ... -

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Basic information

Entry
Database: PDB / ID: 8dd7
TitleThe Cryo-EM structure of Drosophila Cryptochrome in complex with Timeless
Components
  • Methylated-DNA--protein-cysteine methyltransferase,Cryptochrome-1 fusion
  • Protein timeless,Methylated-DNA--protein-cysteine methyltransferase fusion
KeywordsCIRCADIAN CLOCK PROTEIN / Flavoprotein / Nuclear import / Light-sensor / Armadillo-repeat protein
Function / homology
Function and homology information


Nuclear import of PER and TIM / Dephosphorylation of TIM / circadian regulation of heart rate / negative phototaxis / UV-A, blue light phototransduction / photoperiodism / regulation of circadian sleep/wake cycle / magnetoreception / detection of light stimulus involved in magnetoreception / : ...Nuclear import of PER and TIM / Dephosphorylation of TIM / circadian regulation of heart rate / negative phototaxis / UV-A, blue light phototransduction / photoperiodism / regulation of circadian sleep/wake cycle / magnetoreception / detection of light stimulus involved in magnetoreception / : / eclosion rhythm / Transcription repression by PER and activation by PDP1 / Dephosphorylation of PER / gravitaxis / Phosphorylation of PER and TIM / copulation / Degradation of CRY / Degradation of TIM / blue light signaling pathway / circadian temperature homeostasis / rhythmic behavior / regulation of protein import into nucleus / negative regulation of transcription regulatory region DNA binding / response to magnetism / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / replication fork arrest / response to blue light / regulation of circadian sleep/wake cycle, sleep / DNA modification / cellular response to light stimulus / blue light photoreceptor activity / entrainment of circadian clock / DNA replication checkpoint signaling / regulation of phagocytosis / replication fork protection complex / mating behavior / circadian behavior / entrainment of circadian clock by photoperiod / locomotor rhythm / photoreceptor activity / transcription factor binding / response to light stimulus / phototransduction / positive regulation of phagocytosis / FAD binding / circadian regulation of gene expression / regulation of circadian rhythm / circadian rhythm / flavin adenine dinucleotide binding / methylation / protein heterodimerization activity / DNA repair / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Timeless, C-terminal / Timeless PAB domain / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Timeless / Methylated DNA-protein cysteine methyltransferase domain superfamily / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site / Timeless, N-terminal / Timeless protein / Methylated-DNA--protein-cysteine methyltransferase active site. ...Timeless, C-terminal / Timeless PAB domain / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Timeless / Methylated DNA-protein cysteine methyltransferase domain superfamily / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site / Timeless, N-terminal / Timeless protein / Methylated-DNA--protein-cysteine methyltransferase active site. / Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding / Methylated DNA-protein cysteine methyltransferase, DNA binding domain / 6-O-methylguanine DNA methyltransferase, DNA binding domain / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / DNA photolyase, N-terminal / Cryptochrome/photolyase, N-terminal domain superfamily / DNA photolyase / Photolyase/cryptochrome alpha/beta domain profile. / Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily / Rossmann-like alpha/beta/alpha sandwich fold / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Methylated-DNA--protein-cysteine methyltransferase / Cryptochrome-1 / Protein timeless
Similarity search - Component
Biological speciesHomo sapiens (human)
Drosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsFeng, S. / Lin, C. / DeOliveira, C.C. / Crane, B.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122535 United States
CitationJournal: Nature / Year: 2023
Title: Cryptochrome-Timeless structure reveals circadian clock timing mechanisms.
Authors: Changfan Lin / Shi Feng / Cristina C DeOliveira / Brian R Crane /
Abstract: Circadian rhythms influence many behaviours and diseases. They arise from oscillations in gene expression caused by repressor proteins that directly inhibit transcription of their own genes. The fly ...Circadian rhythms influence many behaviours and diseases. 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. 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. 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.
History
DepositionJun 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3May 17, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methylated-DNA--protein-cysteine methyltransferase,Cryptochrome-1 fusion
B: Protein timeless,Methylated-DNA--protein-cysteine methyltransferase fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,6203
Polymers263,8352
Non-polymers7861
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, cross-linking, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Methylated-DNA--protein-cysteine methyltransferase,Cryptochrome-1 fusion


Mass: 83838.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Drosophila melanogaster (fruit fly)
Cell (production host): S2 cell / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: E5BBQ0, UniProt: O77059
#2: Protein Protein timeless,Methylated-DNA--protein-cysteine methyltransferase fusion / 6-O-methylguanine-DNA methyltransferase / O-6-methylguanine-DNA-alkyltransferase


Mass: 179996.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly), (gene. exp.) Homo sapiens (human)
Cell (production host): S2 cell / Production host: Drosophila melanogaster (fruit fly)
References: UniProt: P49021, UniProt: E5BBQ0, methylated-DNA-[protein]-cysteine S-methyltransferase
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of Drosophila Cryptochrome and Timeless / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.264 MDa / Experimental value: YES
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Drosophila melanogaster (fruit fly)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 53 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 160000 / Symmetry type: POINT

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