[English] 日本語
Yorodumi
- PDB-6ae3: Crystal structure of GSK3beta complexed with Morin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ae3
TitleCrystal structure of GSK3beta complexed with Morin
ComponentsGlycogen synthase kinase-3 beta
KeywordsSIGNALING PROTEIN / Kinase / Flavonoid
Function / homology
Function and homology information


hepatic stellate cell activation / B-WICH complex positively regulates rRNA expression / negative regulation of synaptic assembly at neuromuscular junction / negative regulation of neuron maturation / Regulation of HSF1-mediated heat shock response / negative regulation of protein localization to centrosome / re-entry into mitotic cell cycle / Beta-catenin phosphorylation cascade / membrane-bounded organelle / CRMPs in Sema3A signaling ...hepatic stellate cell activation / B-WICH complex positively regulates rRNA expression / negative regulation of synaptic assembly at neuromuscular junction / negative regulation of neuron maturation / Regulation of HSF1-mediated heat shock response / negative regulation of protein localization to centrosome / re-entry into mitotic cell cycle / Beta-catenin phosphorylation cascade / membrane-bounded organelle / CRMPs in Sema3A signaling / Disassembly of the destruction complex and recruitment of AXIN to the membrane / positive regulation of synaptic assembly at neuromuscular junction / positive regulation of osteoclast proliferation / myotube differentiation / cell growth involved in cardiac muscle cell development / negative regulation of neuron migration / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / positive regulation of cardiac muscle cell differentiation / negative regulation of dendrite morphogenesis / Degradation of beta-catenin by the destruction complex / protein localization to microtubule / neuron projection organization / negative regulation of cardiac muscle hypertrophy / beta-catenin destruction complex disassembly / positive regulation of stem cell differentiation / negative regulation of dendrite development / positive regulation of protein localization to cilium / GLI3 is processed to GLI3R by the proteasome / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / autosome genomic imprinting / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / meiosis I / positive regulation of cilium assembly / negative regulation of protein acetylation / bone remodeling / beta-catenin destruction complex / tau-protein kinase / myoblast fusion / regulation of microtubule-based process / regulation of modification of postsynaptic structure / regulation of protein export from nucleus / positive regulation of osteoclast differentiation / axon extension / cellular response to interleukin-3 / Wnt signalosome / negative regulation of protein localization to nucleus / negative regulation of TOR signaling / cellular response to glucocorticoid stimulus / meiotic spindle / regulation of long-term synaptic potentiation / positive regulation of mitochondrial membrane potential / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of calcineurin-NFAT signaling cascade / regulation of osteoblast differentiation / regulation of axon extension / regulation of neuron projection development / establishment or maintenance of cell polarity / cellular response to hepatocyte growth factor stimulus / regulation of dendrite morphogenesis / positive regulation of DNA biosynthetic process / establishment of cell polarity / regulation of axonogenesis / tau-protein kinase activity / dynein complex binding / glycogen metabolic process / response to zinc ion / ER overload response / hepatocyte apoptotic process / fat cell differentiation / positive regulation of osteoblast proliferation / regulation of neuronal synaptic plasticity / negative regulation of smooth muscle cell apoptotic process / positive regulation of excitatory postsynaptic potential / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / epithelial to mesenchymal transition / canonical Wnt signaling pathway / positive regulation of axon extension / positive regulation of autophagy / regulation of microtubule cytoskeleton organization / protein serine/threonine kinase binding / extrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway in absence of ligand / cytoskeleton organization / negative regulation of insulin receptor signaling pathway / protein export from nucleus / axonogenesis / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein export from nucleus / positive regulation of peptidyl-threonine phosphorylation / dendritic shaft / stem cell differentiation / regulation of cell growth / animal organ morphogenesis / positive regulation of smooth muscle cell proliferation / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / negative regulation of canonical Wnt signaling pathway / tau protein binding
Similarity search - Function
Glycogen synthase kinase 3, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Glycogen synthase kinase 3, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-MRI / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsKim, K.L. / Cha, J.S. / Kim, J.S. / Ahn, J.S. / Ha, N.C. / Cho, H.S.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Crystal structure of GSK3 beta in complex with the flavonoid, morin
Authors: Kim, K. / Cha, J.S. / Kim, J.S. / Ahn, J. / Ha, N.C. / Cho, H.S.
History
DepositionAug 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycogen synthase kinase-3 beta
B: Glycogen synthase kinase-3 beta
C: Glycogen synthase kinase-3 beta
D: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,36210
Polymers187,3894
Non-polymers9736
Water7,602422
1
A: Glycogen synthase kinase-3 beta
B: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4836
Polymers93,6942
Non-polymers7894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glycogen synthase kinase-3 beta
D: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8794
Polymers93,6942
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.588, 134.360, 100.393
Angle α, β, γ (deg.)90.00, 103.80, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Glycogen synthase kinase-3 beta / GSK-3 beta / Serine/threonine-protein kinase GSK3B


Mass: 46847.184 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Tyrosine 217 is phosphorylated. / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gsk3b / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9WV60, tau-protein kinase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-MRI / 2-[2,4-bis(oxidanyl)phenyl]-3,5,7-tris(oxidanyl)chromen-4-one / Morin


Mass: 302.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM Sodium Citrate (pH6.5), 18%(v/v) PEG 4000, 5%(v/v) 2-propanol

-
Data collection

DiffractionMean temperature: 83 K / Ambient temp details: 83
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.987 Å
DetectorType: RIGAKU / Detector: CCD / Date: Jun 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 93509 / % possible obs: 97.8 % / Redundancy: 6 % / Net I/σ(I): 38.17
Reflection shellResolution: 2.14→2.18 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→40 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.14 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.174 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22626 4608 4.9 %RANDOM
Rwork0.1906 ---
obs0.19236 88879 97.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.981 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å21.2 Å2
2--0.74 Å20 Å2
3----0.41 Å2
Refinement stepCycle: 1 / Resolution: 2.14→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10463 0 68 422 10953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01410789
X-RAY DIFFRACTIONr_bond_other_d0.0030.0179620
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.67614754
X-RAY DIFFRACTIONr_angle_other_deg0.9691.63222419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.19951339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2221.394495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.678151610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5551567
X-RAY DIFFRACTIONr_chiral_restr0.0760.21460
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212008
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021978
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9344.8275412
X-RAY DIFFRACTIONr_mcbond_other3.9324.8265411
X-RAY DIFFRACTIONr_mcangle_it5.6067.2096731
X-RAY DIFFRACTIONr_mcangle_other5.6067.216732
X-RAY DIFFRACTIONr_scbond_it4.1714.9585377
X-RAY DIFFRACTIONr_scbond_other4.1684.9585377
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0787.3658024
X-RAY DIFFRACTIONr_long_range_B_refined9.04388.81644513
X-RAY DIFFRACTIONr_long_range_B_other9.03588.89344226
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.14→2.195 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 309 -
Rwork0.268 6267 -
obs--93.37 %

+
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://pdbjlvh1.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