[English] 日本語
Yorodumi
- PDB-6lue: Crystal structure of mouse Cryptochrome 1 in complex with compoun... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lue
TitleCrystal structure of mouse Cryptochrome 1 in complex with compound KL201
ComponentsCryptochrome-1
KeywordsCIRCADIAN CLOCK PROTEIN / Cryptochrome / CRY / circadian clock / KL201
Function / homology
Function and homology information


negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor signaling pathway / negative regulation of circadian rhythm / lipid storage / regulation of DNA damage checkpoint / response to glucagon / negative regulation of G protein-coupled receptor signaling pathway / regulation of gluconeogenesis / entrainment of circadian clock by photoperiod / E-box binding ...negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor signaling pathway / negative regulation of circadian rhythm / lipid storage / regulation of DNA damage checkpoint / response to glucagon / negative regulation of G protein-coupled receptor signaling pathway / regulation of gluconeogenesis / entrainment of circadian clock by photoperiod / E-box binding / photoreceptor activity / response to light stimulus / signal transduction in response to DNA damage / phosphatase binding / negative regulation of gluconeogenesis / positive regulation of gluconeogenesis / negative regulation of protein ubiquitination / FAD binding / positive regulation of protein ubiquitination / gluconeogenesis / response to activity / nuclear receptor binding / circadian regulation of gene expression / response to insulin / regulation of circadian rhythm / kinase binding / histone deacetylase binding / circadian rhythm / glucose homeostasis / double-stranded DNA binding / DNA-binding transcription factor binding / negative regulation of DNA-templated transcription / protein kinase binding / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / 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. ...DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / 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 / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-EUL / Cryptochrome-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMiller, S. / Aikawa, Y. / Hirota, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJPR14LA Japan
Japan Society for the Promotion of Science (JSPS)15H05590 Japan
Japan Society for the Promotion of Science (JSPS)18H02402 Japan
CitationJournal: Cell Chem Biol / Year: 2020
Title: An Isoform-Selective Modulator of Cryptochrome 1 Regulates Circadian Rhythms in Mammals.
Authors: Miller, S. / Aikawa, Y. / Sugiyama, A. / Nagai, Y. / Hara, A. / Oshima, T. / Amaike, K. / Kay, S.A. / Itami, K. / Hirota, T.
History
DepositionJan 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cryptochrome-1
B: Cryptochrome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,5204
Polymers114,7432
Non-polymers7772
Water7,098394
1
A: Cryptochrome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7602
Polymers57,3721
Non-polymers3881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cryptochrome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7602
Polymers57,3721
Non-polymers3881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.551, 143.260, 76.730
Angle α, β, γ (deg.)90.000, 118.650, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein Cryptochrome-1


Mass: 57371.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cry1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P97784
#2: Chemical ChemComp-EUL / 2-bromanyl-N-(5,6,7,8-tetrahydro-[1]benzothiolo[2,3-d]pyrimidin-4-yl)benzamide


Mass: 388.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H14BrN3OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% w/v PEG 3350, 3% v/v ethylene glycol, 200 mM NH4Cl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→41.45 Å / Num. obs: 71867 / % possible obs: 99.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 19.14 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.091 / Net I/σ(I): 6.6
Reflection shellResolution: 2.1→2.175 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 10493 / CC1/2: 0.545 / Rpim(I) all: 0.31

-
Processing

Software
NameVersionClassification
REFMAC5refinement
PHENIX1.17.1_3660refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K0R

4k0r


Resolution: 2.1→40.46 Å / SU ML: 0.2879 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.7025
RfactorNum. reflection% reflection
Rfree0.2556 3577 4.98 %
Rwork0.2184 --
obs0.2203 71826 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7344 0 46 394 7784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00527598
X-RAY DIFFRACTIONf_angle_d0.661310356
X-RAY DIFFRACTIONf_chiral_restr0.04331122
X-RAY DIFFRACTIONf_plane_restr0.00471324
X-RAY DIFFRACTIONf_dihedral_angle_d8.28291018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.33041300.28222631X-RAY DIFFRACTION99.86
2.13-2.160.29391430.25322597X-RAY DIFFRACTION99.96
2.16-2.190.2861570.24162612X-RAY DIFFRACTION100
2.19-2.220.27961400.24652610X-RAY DIFFRACTION99.96
2.22-2.250.3691480.30292607X-RAY DIFFRACTION99.17
2.25-2.290.31951210.25982603X-RAY DIFFRACTION99.82
2.29-2.330.29851500.23552624X-RAY DIFFRACTION99.96
2.33-2.370.27811300.22412617X-RAY DIFFRACTION99.93
2.37-2.420.27111390.22072641X-RAY DIFFRACTION100
2.42-2.470.27131490.21812608X-RAY DIFFRACTION99.96
2.47-2.520.26671520.21872596X-RAY DIFFRACTION99.96
2.52-2.580.25711290.22242638X-RAY DIFFRACTION100
2.58-2.650.27521470.23022611X-RAY DIFFRACTION99.89
2.65-2.720.26361460.22442636X-RAY DIFFRACTION99.93
2.72-2.80.2651270.22022601X-RAY DIFFRACTION99.96
2.8-2.890.29391210.21992664X-RAY DIFFRACTION99.96
2.89-2.990.25851260.2252632X-RAY DIFFRACTION99.93
2.99-3.110.2731370.21192668X-RAY DIFFRACTION99.89
3.11-3.250.23271580.22192583X-RAY DIFFRACTION99.89
3.25-3.420.2521440.2192612X-RAY DIFFRACTION99.86
3.42-3.640.2311150.20572663X-RAY DIFFRACTION99.86
3.64-3.920.23681310.18832637X-RAY DIFFRACTION99.71
3.92-4.310.21071450.18472610X-RAY DIFFRACTION99.75
4.31-4.940.20811480.19222627X-RAY DIFFRACTION99.5
4.94-6.210.24541180.21392655X-RAY DIFFRACTION99.39
6.22-40.460.21341260.20942666X-RAY DIFFRACTION98.31
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.246-0.368-0.2661.0450.0580.72-0.0419-0.189-0.069-0.00940.0780.0173-0.0016-0.0054-0.0120.07150.0117-0.01120.1330.0220.114135.5612.82774.019
20.926-0.083-0.250.897-0.1090.4320.0406-0.016-0.02720.00050.0220.0506-0.102-0.119-0.03940.09590.028-0.00710.1210.00050.114113.40523.29367.426
30.63-0.0592-0.00981.076-0.4270.991-0.0492-0.03870.0391-0.01110.0787-0.0127-0.0617-0.137-0.03080.1290.0303-0.0150.1390.00890.11398.75438.51494.493
40.391-0.261-0.03030.677-0.2291.096-0.125-0.13-0.03780.1350.0662-0.01740.0131-0.02040.02690.1630.03330.00480.1650.01540.111110.73119.428111.71
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 301
2X-RAY DIFFRACTION2A302 - 492
3X-RAY DIFFRACTION3B0 - 261
4X-RAY DIFFRACTION4B262 - 492

+
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