[English] 日本語
Yorodumi
- PDB-8dd7: The Cryo-EM structure of Drosophila Cryptochrome in complex with ... -

+
Open data


ID or keywords:

Loading...

-
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 / regulation of circadian sleep/wake cycle / magnetoreception / detection of light stimulus involved in magnetoreception / eclosion rhythm / Transcription repression by PER and activation by PDP1 ...Nuclear import of PER and TIM / Dephosphorylation of TIM / circadian regulation of heart rate / negative phototaxis / UV-A, blue light phototransduction / 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 / photoperiodism / Phosphorylation of PER and TIM / copulation / Degradation of CRY / Degradation of TIM / circadian temperature homeostasis / blue light signaling pathway / rhythmic behavior / regulation of protein import into nucleus / response to magnetism / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / replication fork arrest / regulation of circadian sleep/wake cycle, sleep / cellular response to light stimulus / blue light photoreceptor activity / response to blue light / replication fork protection complex / entrainment of circadian clock / DNA replication checkpoint signaling / regulation of phagocytosis / circadian behavior / mating behavior / entrainment of circadian clock by photoperiod / locomotor rhythm / response to light stimulus / photoreceptor activity / phototransduction / FAD binding / positive regulation of phagocytosis / circadian regulation of gene expression / circadian rhythm / regulation of circadian rhythm / flavin adenine dinucleotide binding / methylation / DNA repair / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / DNA binding / nucleoplasm / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Timeless, C-terminal / Timeless PAB domain / Timeless, N-terminal / Timeless / Timeless protein / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Methylated DNA-protein cysteine methyltransferase domain superfamily / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site / Methylated-DNA--protein-cysteine methyltransferase active site. ...Timeless, C-terminal / Timeless PAB domain / Timeless, N-terminal / Timeless / Timeless protein / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Methylated DNA-protein cysteine methyltransferase domain superfamily / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site / 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
Revision 1.4Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
1


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

-
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


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

-
Experimental details

-
Experiment

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

-
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

-
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 FIELD / 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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more