[English] 日本語
Yorodumi
- PDB-6qtw: Crystal structure of an Arabidopsis WD40 domain in complex with a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qtw
TitleCrystal structure of an Arabidopsis WD40 domain in complex with a blue light photoreceptor
Components
  • Cryptochrome-1
  • E3 ubiquitin-protein ligase COP1
KeywordsPLANT PROTEIN / Complex
Function / homology
Function and homology information


detection of light stimulus / photoprotection / singlet oxygen-mediated programmed cell death / negative regulation of lateral root development / positive regulation of shade avoidance / positive regulation of systemic acquired resistance / regulation of secondary cell wall biogenesis / regulation of unidimensional cell growth / response to red light / auxin transport ...detection of light stimulus / photoprotection / singlet oxygen-mediated programmed cell death / negative regulation of lateral root development / positive regulation of shade avoidance / positive regulation of systemic acquired resistance / regulation of secondary cell wall biogenesis / regulation of unidimensional cell growth / response to red light / auxin transport / flavin adenine dinucleotide metabolic process / plant organ development / response to absence of light / circadian regulation of calcium ion oscillation / anthocyanin-containing compound metabolic process / response to strigolactone / regulation of meristem growth / response to low fluence blue light stimulus by blue low-fluence system / shade avoidance / regulation of leaf morphogenesis / positive regulation of flavonoid biosynthetic process / blue light signaling pathway / skotomorphogenesis / photoperiodism, flowering / red, far-red light phototransduction / positive regulation of anion channel activity / response to high light intensity / response to far red light / response to magnetism / phototropism / photomorphogenesis / stomatal movement / positive regulation of defense response to bacterium / response to blue light / regulation of stomatal movement / blue light photoreceptor activity / regulation of hydrogen peroxide metabolic process / nuclear ubiquitin ligase complex / response to water deprivation / entrainment of circadian clock / Cul4-RING E3 ubiquitin ligase complex / response to UV-B / regulation of reactive oxygen species metabolic process / response to temperature stimulus / response to light stimulus / FAD binding / RING-type E3 ubiquitin transferase / defense response / regulation of circadian rhythm / PML body / circadian rhythm / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / kinase activity / regulation of gene expression / protein autophosphorylation / protein ubiquitination / nuclear body / protein kinase activity / DNA repair / protein homodimerization activity / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cryptochrome C-terminal / Blue/Ultraviolet sensing protein C terminal / Cryptochrome, plant / E3 ubiquitin-protein ligase COP1 / DNA photolyases class 1 signature 2. / Cryptochrome/DNA photolyase class 1, conserved site, C-terminal / DNA photolyases class 1 signature 1. / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase ...Cryptochrome C-terminal / Blue/Ultraviolet sensing protein C terminal / Cryptochrome, plant / E3 ubiquitin-protein ligase COP1 / DNA photolyases class 1 signature 2. / Cryptochrome/DNA photolyase class 1, conserved site, C-terminal / DNA photolyases class 1 signature 1. / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / Zinc finger, C3HC4 type (RING finger) / 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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Ring finger / Rossmann-like alpha/beta/alpha sandwich fold / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
MALONATE ION / E3 ubiquitin-protein ligase COP1 / Cryptochrome-1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsHothorn, M. / Lau, K.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_175774 Switzerland
European Communitys Seventh Framework Programme310539 Switzerland
European Molecular Biology OrganizationALTF 493-2015 Switzerland
CitationJournal: Embo J. / Year: 2019
Title: Plant photoreceptors and their signaling components compete for COP1 binding via VP peptide motifs.
Authors: Lau, K. / Podolec, R. / Chappuis, R. / Ulm, R. / Hothorn, M.
History
DepositionFeb 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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: E3 ubiquitin-protein ligase COP1
B: Cryptochrome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8176
Polymers38,4292
Non-polymers3884
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-2 kcal/mol
Surface area12610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.620, 55.142, 103.155
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 E3 ubiquitin-protein ligase COP1 / Constitutive photomorphogenesis protein 1 / RING-type E3 ubiquitin transferase COP1


Mass: 37220.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: COP1, At2g32950, T21L14.11 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P43254, RING-type E3 ubiquitin transferase
#2: Protein/peptide Cryptochrome-1 / / Atcry1 / Blue light photoreceptor / Protein BLUE LIGHT UNINHIBITED 1 / Protein ELONGATED HYPOCOTYL ...Atcry1 / Blue light photoreceptor / Protein BLUE LIGHT UNINHIBITED 1 / Protein ELONGATED HYPOCOTYL 4 / Protein OUT OF PHASE 2 / OOP2


Mass: 1208.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q43125
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.86 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: 5 mg/mL of COP1 supplemented with 3 to 10 fold molar excess in peptide was mixed with two-fold (v/v) more mother liquor (1:2 ratio; protein:buffer) containing 1.25 M sodium malonate pH 7.5.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.39→43.98 Å / Num. obs: 56339 / % possible obs: 99.88 % / Redundancy: 12.7 % / Biso Wilson estimate: 10.9 Å2 / Rrim(I) all: 0.0561 / Net I/σ(I): 11.78
Reflection shellResolution: 1.39→1.44 Å

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IGO

5igo


Resolution: 1.39→43.98 Å / SU ML: 0.1436 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.0895
RfactorNum. reflection% reflection
Rfree0.1723 2762 4.9 %
Rwork0.1361 --
obs0.1379 56337 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 15.64 Å2
Refinement stepCycle: LAST / Resolution: 1.39→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2449 0 26 280 2755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782658
X-RAY DIFFRACTIONf_angle_d1.05633629
X-RAY DIFFRACTIONf_chiral_restr0.0888412
X-RAY DIFFRACTIONf_plane_restr0.0062462
X-RAY DIFFRACTIONf_dihedral_angle_d16.84721015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.420.28681390.22972582X-RAY DIFFRACTION98.09
1.42-1.440.2661250.21572635X-RAY DIFFRACTION100
1.44-1.470.29361360.19522660X-RAY DIFFRACTION99.64
1.47-1.50.2431440.18022632X-RAY DIFFRACTION99.93
1.5-1.530.20411440.16392645X-RAY DIFFRACTION100
1.53-1.570.21111360.15022640X-RAY DIFFRACTION99.96
1.57-1.610.1981210.14042660X-RAY DIFFRACTION100
1.61-1.650.20831470.13562634X-RAY DIFFRACTION100
1.65-1.70.18161210.13222674X-RAY DIFFRACTION100
1.7-1.750.17331330.12862662X-RAY DIFFRACTION100
1.75-1.820.15271320.11942672X-RAY DIFFRACTION99.96
1.82-1.890.15721640.11772681X-RAY DIFFRACTION100
1.89-1.970.15091380.11732648X-RAY DIFFRACTION100
1.97-2.080.14751210.11322696X-RAY DIFFRACTION100
2.08-2.210.15151530.10962683X-RAY DIFFRACTION100
2.21-2.380.14321260.11852708X-RAY DIFFRACTION100
2.38-2.620.17071510.12232692X-RAY DIFFRACTION100
2.62-30.13771320.13142730X-RAY DIFFRACTION100
3-3.780.15511400.12872759X-RAY DIFFRACTION100
3.78-440.17861590.15562882X-RAY DIFFRACTION100

+
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