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- EMDB-27335: The Cryo-EM structure of Drosophila Cryptochrome in complex with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-27335
TitleThe Cryo-EM structure of Drosophila Cryptochrome in complex with Timeless
Map data
Sample
  • Complex: Complex of Drosophila Cryptochrome and Timeless
    • Protein or peptide: Methylated-DNA--protein-cysteine methyltransferase,Cryptochrome-1 fusion
  • Protein or peptide: Protein timeless,Methylated-DNA--protein-cysteine methyltransferase fusion
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDEFlavin adenine dinucleotide
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
Methylated-DNA--protein-cysteine methyltransferase / Cryptochrome-1 / Protein timeless
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsFeng S / Lin C / DeOliveira CC / Crane BR
Funding support United States, 1 items
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, 2022-
Header (metadata) releaseFeb 15, 2023-
Map releaseFeb 15, 2023-
UpdateMay 17, 2023-
Current statusMay 17, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27335.png

Downloads & links

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Map

FileDownload / File: emd_27335.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.032 Å
Density
Contour LevelBy AUTHOR: 12.4
Minimum - Maximum-21.703703 - 53.32844
Average (Standard dev.)-5.79668e-12 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 309.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_27335_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_27335_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27335_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of Drosophila Cryptochrome and Timeless

EntireName: Complex of Drosophila Cryptochrome and Timeless
Components
  • Complex: Complex of Drosophila Cryptochrome and Timeless
    • Protein or peptide: Methylated-DNA--protein-cysteine methyltransferase,Cryptochrome-1 fusion
  • Protein or peptide: Protein timeless,Methylated-DNA--protein-cysteine methyltransferase fusion
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDEFlavin adenine dinucleotide

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Supramolecule #1: Complex of Drosophila Cryptochrome and Timeless

SupramoleculeName: Complex of Drosophila Cryptochrome and Timeless / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 264 KDa

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Macromolecule #1: Methylated-DNA--protein-cysteine methyltransferase,Cryptochrome-1...

MacromoleculeName: Methylated-DNA--protein-cysteine methyltransferase,Cryptochrome-1 fusion
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 83.838617 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: MEQKLISEED LGGGEQKLIS EEDLGGGEQK LISEEDLGGG MDKDCEMKRT TLDSPLGKLE LSGCEQGLHR IIFLGKGTSA ADAVEVPAP AAVLGGPEPL IQATAWLNAY FHQPEAIEEF PVPALHHPVF QQESFTRQVL WKLLKVVKFG EVISESHLAA L VGNPAATA ...String:
MEQKLISEED LGGGEQKLIS EEDLGGGEQK LISEEDLGGG MDKDCEMKRT TLDSPLGKLE LSGCEQGLHR IIFLGKGTSA ADAVEVPAP AAVLGGPEPL IQATAWLNAY FHQPEAIEEF PVPALHHPVF QQESFTRQVL WKLLKVVKFG EVISESHLAA L VGNPAATA AVNTALDGNP VPILIPCHRV VQGDSDVGPY LGGLAVKEWL LAHEGHRLGK PGLGGGSGMA TRGANVIWFR HG LRLHDNP ALLAALADKD QGIALIPVFI FDGESAGTKN VGYNRMRFLL DSLQDIDDQL QAATDGRGRL LVFEGEPAYI FRR LHEQVR LHRICIEQDC EPIWNERDES IRSLCRELNI DFVEKVSHTL WDPQLVIETN GGIPPLTYQM FLHTVQIIGL PPRP TADAR LEDATFVELD PEFCRSLKLF EQLPTPEHFN VYGDNMGFLA KINWRGGETQ ALLLLDERLK VEQHAFERGF YLPNQ ALPN IHDSPKSMSA HLRFGCLSVR RFYWSVHDLF KNVQLRACVR GVQMTGGAHI TGQLIWREYF YTMSVNNPNY DRMEGN DIC LSIPWAKPNE NLLQSWRLGQ TGFPLIDGAM RQLLAEGWLH HTLRNTVATF LTRGGLWQSW EHGLQHFLKY LLDADWS VC AGNWMWVSSS AFERLLDSSL VTCPVALAKR LDPDGTYIKQ YVPELMNVPK EFVHEPWRMS AEQQEQYECL IGVHYPER I IDLSMAVKRN MLAMKSLRNS LITPP

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Macromolecule #2: Protein timeless,Methylated-DNA--protein-cysteine methyltransfera...

MacromoleculeName: Protein timeless,Methylated-DNA--protein-cysteine methyltransferase fusion
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: methylated-DNA-[protein]-cysteine S-methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 179.996109 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: MDWLLATPQL YSAFSSLGCL EGDTYVVNPN ALAILEEINY KLTYEDQTLR TFRRAIGFGQ NVRSDLIPLL ENAKDDAVLE SVIRILVNL TVPVECLFSV DVMYRTDVGR HTIFELNKLL YTSKEAFTEA RSTKSVVEYM KHILESDPKL SPHKCDQINN C LLLLRNIL ...String:
MDWLLATPQL YSAFSSLGCL EGDTYVVNPN ALAILEEINY KLTYEDQTLR TFRRAIGFGQ NVRSDLIPLL ENAKDDAVLE SVIRILVNL TVPVECLFSV DVMYRTDVGR HTIFELNKLL YTSKEAFTEA RSTKSVVEYM KHILESDPKL SPHKCDQINN C LLLLRNIL HIPETHAHCV MPMMQSMPHG ISMQNTILWN LFIQSIDKLL LYLMTCPQRA FWGVTMVQLI ALIYKDQHVS TL QKLLSLW FEASLSESSE DNESNTSPPK QGSGDSSPML TSDPTSDSSD NGSNGRGMGG GMREGTAATL QEVSRKGQEY QNA MARVPA DKPDGSEEAS DMTGNDSEQP GSPEQSQPAG ESMDDGDYED QRHRQLNEHG EEDEDEDEVE EEEYLQLGPA SEPL NLTQQ PADKVNNTTN PTSSAPQGCL GNEPFKPPPP LPVRASTSAH AQMQKFNESS YASHVSAVKL GQKSPHAGQL QLTKG KCCP QKRECPSSQS ELSDCGYGTQ VENQESISTS SNDDDGPQGK PQHQKPPCNT KPRNKPRTIM SPMDKKELRR KKLVKR SKS SLINMKGLVQ HTPTDDDISN LLKEFTVDFL LKGYSYLVEE LHMQLLSNAK VPIDTSHFFW LVTYFLKFAA QLELDME HI DTILTYDVLS YLTYEGVSLC EQLELNARQE GSDLKPYLRR MHLVVTAIRE FLQAIDTYNK VTHLNEDDKA HLRQLQLQ I SEMSDLRCLF VLLLRRFNPS IHSKQYLQDL VVTNHILLLI LDSSAKLGGC QTIRLSEHIT QFATLEVMHY YGILLEDFN NNGEFVNDCI FTMMHHIGGD LGQIGVLFQP IILKTYSRIW EADYELCDDW SDLIEYVIHK FMNTPPKSPL TIPTTSLTEM TKEHNQEHT VCSWSQEEMD TLYWYYVQSK KNNDIVGKIV KLFSNNGNKL KTRISIIQQL LQQDIITLLE YDDLMKFEDA E YQRTLLTT PTSATTESGI EIKECAYGKP SDDVQILLDL IIKENKAQHL LWLQRILIEC CFVKLTLRSG LKVPEGDHIM EP VAYHCIC KQKSIPVVQW NNEQSTTMLY QPFVLLLHKL GIQLPADAGS IFARIPDYWT PETMYGLAKK LGPLDKLNLK FDA SELEDA TASSPSRYHH TGPRNSLSSV SSLDVDLGDT EELALIPEVD AAVEKAHAMA STPSPSEIFA VPKTKHCNSI IRYT PDPTP PVPNWLQLVM RSKCNHRTGP SGDPSDCIGS SSTTVDDEGF GKSISAATSQ AASTSMSTVN PTTTLSLNML NTFMG SHNE NSSSSGCGGT VSSLSMVALM STGAAGGGGN TSGLEMDVDA SMKSSFERLE VNGSHFSRAN NLDQEYSAMV ASVYEK EKE LNSDNVSLAS DLTRMYVSDE DDRLERTEIR VPHYHLEGGS GMDKDCEMKR TTLDSPLGKL ELSGCEQGLH RIIFLGK GT SAADAVEVPA PAAVLGGPEP LMQATAWLNA YFHQPEAIEE FPVPALHHPV FQQESFTRQV LWKLLKVVKF GEVISYSH L AALAGNPAAT AAVKTALSGN PVPILIPCHR VVQGDLDVGG YEGGLAVKEW LLAHEGHRLG KPGLGGGGYP YDVPDYART GGGSGSRLEE ELRRRLTE

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Macromolecule #3: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 1 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM / Flavin adenine dinucleotide

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4gu5

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 160000
FSC plot (resolution estimation)

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