[English] 日本語
Yorodumi
- PDB-7wva: Crystal structure of mouse Cryptochrome 1 in complex with TH401 c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7wva
TitleCrystal structure of mouse Cryptochrome 1 in complex with TH401 compound
ComponentsCryptochrome-1
KeywordsCIRCADIAN CLOCK PROTEIN / circadian / clock / cryptochrome / CRY / CRY1
Function / homology
Function and homology information


negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor signaling pathway / negative regulation of circadian rhythm / negative regulation of G protein-coupled receptor signaling pathway / lipid storage / regulation of DNA damage checkpoint / response to glucagon / 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 / negative regulation of G protein-coupled receptor signaling pathway / lipid storage / regulation of DNA damage checkpoint / response to glucagon / regulation of gluconeogenesis / entrainment of circadian clock by photoperiod / E-box binding / photoreceptor activity / response to light stimulus / phosphatase binding / negative regulation of gluconeogenesis / signal transduction in response to DNA damage / positive regulation of gluconeogenesis / negative regulation of protein ubiquitination / FAD binding / response to activity / positive regulation of protein ubiquitination / gluconeogenesis / nuclear receptor binding / circadian regulation of gene expression / response to insulin / regulation of circadian rhythm / kinase binding / circadian rhythm / histone deacetylase binding / 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
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
Similarity search - Domain/homology
Chem-6I3 / Cryptochrome-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMiller, S.A. / Hirota, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H02402 Japan
Japan Society for the Promotion of Science (JSPS)21H04766 Japan
Citation
Journal: F1000Res / Year: 2022
Title: A methylbenzimidazole derivative regulates mammalian circadian rhythms by targeting Cryptochrome proteins.
Authors: Yagi, M. / Miller, S. / Nagai, Y. / Inuki, S. / Sato, A. / Hirota, T.
#1: Journal: F1000Res / Year: 2022
Title: A methylbenzimidazole derivative regulates mammalian circadian rhythms by targeting Cryptochrome proteins
Authors: Moeri, Y. / Miller, S. / Nagai, Y. / Inuk, S. / Sato, A. / Hirota, T.
History
DepositionFeb 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Oct 26, 2022Group: Database references / Category: citation / citation_author
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cryptochrome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7862
Polymers57,3721
Non-polymers4141
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The protein is monomeric in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20220 Å2
Unit cell
Length a, b, c (Å)44.916, 78.195, 132.818
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Cryptochrome-1 /


Mass: 57371.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cry1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P97784
#2: Chemical ChemComp-6I3 / 2-(1-methylbenzimidazol-2-yl)sulfanyl-N-[(E)-(2,3,4-trimethoxyphenyl)methylideneamino]ethanamide


Mass: 414.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N4O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.04 Å3/Da / Density % sol: 39.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.25 M NH4Cl, 22% w/v PEG 3350, 3% v/v Ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→78.18 Å / Num. obs: 30136 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 31.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.03 / Rrim(I) all: 0.083 / Net I/σ(I): 13.7
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 3 / Num. unique obs: 4271 / CC1/2: 0.891 / Rpim(I) all: 0.187 / Rrim(I) all: 0.512 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
REFMAC5.8.0257refinement
xia2data reduction
SCALA3.3.22data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KX4

6kx4


Resolution: 2.05→67.38 Å / SU ML: 0.2457 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2044
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2204 1456 4.84 %
Rwork0.1897 28612 -
obs0.1911 30068 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.06 Å2
Refinement stepCycle: LAST / Resolution: 2.05→67.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3640 0 29 171 3840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00723777
X-RAY DIFFRACTIONf_angle_d0.77875169
X-RAY DIFFRACTIONf_chiral_restr0.0481564
X-RAY DIFFRACTIONf_plane_restr0.0077665
X-RAY DIFFRACTIONf_dihedral_angle_d19.59931282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.120.29311500.23342752X-RAY DIFFRACTION98.94
2.12-2.210.25951490.20942797X-RAY DIFFRACTION99.66
2.21-2.310.26011540.21382804X-RAY DIFFRACTION99.7
2.31-2.430.23681510.19252841X-RAY DIFFRACTION99.93
2.43-2.580.26211590.1862802X-RAY DIFFRACTION99.93
2.58-2.780.24491440.19512854X-RAY DIFFRACTION99.9
2.78-3.060.2431210.20462883X-RAY DIFFRACTION99.97
3.06-3.510.23171470.1892892X-RAY DIFFRACTION100
3.51-4.420.17191400.16332906X-RAY DIFFRACTION100
4.42-67.380.19411410.19153081X-RAY DIFFRACTION99.97
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)
11.5877959206-0.32619479672-0.05363963300452.08247149928-0.1236013145182.55708043629-0.0335102352149-0.2328152654160.0005120208955780.2063560794070.0957382644173-0.01674067173690.0950120966017-0.353482431993-0.05797457479080.199658231638-0.0116141480623-0.02375829985120.251974888014-0.0230280651820.204351715357-4.956864133476.06159947491-11.5261350106
20.6611692359950.2521438160660.06408010546512.63632158699-0.2253335174951.521369489910.0725424584788-0.1048741089480.2054120003120.0975411030114-0.06859914940520.104939606512-0.414720151112-0.0009009295574680.058749410470.281165929063-0.00325314173280.01237845605340.194641966452-0.04501044251550.3064568289465.1695949252423.5039472557-21.1174728065
32.18953101578-0.515620974317-0.1856152594741.4368536082-0.1309900901121.099272448870.2272389421210.392345721520.00617446601333-0.254928732649-0.1784359239640.0173783760543-0.153301171193-0.24429084434-0.05841355172670.2581592520940.0909536593346-0.01046594245840.266126103553-0.03071124420530.22195803179-7.6145897099315.7523006859-41.1696272408
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 229 )2 - 2291 - 223
22chain 'A' and (resid 230 through 283 )230 - 283224 - 275
33chain 'A' and (resid 284 through 494 )284 - 494276 - 480

+
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