[English] 日本語
Yorodumi
- PDB-7z1g: Crystal structure of nonphosphorylated (Tyr216) GSK3b in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7z1g
TitleCrystal structure of nonphosphorylated (Tyr216) GSK3b in complex with CX-4945
ComponentsGlycogen synthase kinase-3 beta
KeywordsTRANSFERASE / Kinase / diabetes / kinase inhibitor
Function / homology
Function and homology information


neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of type B pancreatic cell development / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of TORC2 signaling / negative regulation of dopaminergic neuron differentiation ...neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of type B pancreatic cell development / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of TORC2 signaling / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / positive regulation of protein localization to centrosome / positive regulation of cilium assembly / CRMPs in Sema3A signaling / heart valve development / tau-protein kinase / beta-catenin destruction complex / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / regulation of protein export from nucleus / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / cellular response to interleukin-3 / Maturation of nucleoprotein / Wnt signalosome / regulation of long-term synaptic potentiation / negative regulation of TOR signaling / negative regulation of protein localization to nucleus / regulation of microtubule-based process / AKT phosphorylates targets in the cytosol / Disassembly of the destruction complex and recruitment of AXIN to the membrane / negative regulation of calcineurin-NFAT signaling cascade / regulation of axon extension / Maturation of nucleoprotein / tau-protein kinase activity / negative regulation of epithelial to mesenchymal transition / G protein-coupled dopamine receptor signaling pathway / positive regulation of cell-matrix adhesion / regulation of axonogenesis / regulation of dendrite morphogenesis / glycogen metabolic process / ER overload response / regulation of neuron projection development / Constitutive Signaling by AKT1 E17K in Cancer / establishment of cell polarity / protein kinase A catalytic subunit binding / dynactin binding / epithelial to mesenchymal transition / Regulation of HSF1-mediated heat shock response / canonical Wnt signaling pathway / NF-kappaB binding / negative regulation of osteoblast differentiation / positive regulation of protein binding / negative regulation of protein-containing complex assembly / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of cellular response to heat / extrinsic apoptotic signaling pathway / cellular response to retinoic acid / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of autophagy / presynaptic modulation of chemical synaptic transmission / Transcriptional and post-translational regulation of MITF-M expression and activity / regulation of microtubule cytoskeleton organization / negative regulation of cell migration / response to endoplasmic reticulum stress / positive regulation of protein export from nucleus / positive regulation of protein ubiquitination / Ubiquitin-dependent degradation of Cyclin D / mitochondrion organization / excitatory postsynaptic potential / hippocampus development / positive regulation of cell differentiation / positive regulation of protein-containing complex assembly / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / negative regulation of canonical Wnt signaling pathway / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / circadian rhythm / regulation of circadian rhythm / Degradation of beta-catenin by the destruction complex / beta-catenin binding / peptidyl-serine phosphorylation / B-WICH complex positively regulates rRNA expression / tau protein binding / Wnt signaling pathway / cellular response to amyloid-beta / neuron projection development / Regulation of RUNX2 expression and activity / positive regulation of protein catabolic process / p53 binding / kinase activity / insulin receptor signaling pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of neuron apoptotic process
Similarity search - Function
Glycogen synthase kinase 3, catalytic domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Glycogen synthase kinase 3, catalytic domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-3NG / IMIDAZOLE / MALONATE ION / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsGrygier, P. / Pustelny, K. / Dubin, G. / Czarna, A.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science Centre2019/34/E/NZ1/00467 Poland
National Center for Research and Development (Poland)PPN/PPO/2018/1/00046 Poland
CitationJournal: To Be Published
Title: Crystal structure of nonphosphorylated (Tyr216) GSK3b kinase in complex with CX-4945
Authors: Grygier, P. / Pustelny, K. / Golik, P. / Popowicz, G. / Dubin, G. / Czarna, A.
History
DepositionFeb 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,5039
Polymers41,5051
Non-polymers9988
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.812, 84.812, 195.968
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

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


Mass: 41504.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSK3B / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR
References: UniProt: P49841, tau-protein kinase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-3NG / 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid


Mass: 349.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H12ClN3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 4.23 Å3/Da / Density % sol: 70.96 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1.0 M Sodium acetate trihydrate 0.1 M Imidazole pH 6.5, 0.2 M di-Sodium malonate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.85→44.18 Å / Num. obs: 17331 / % possible obs: 99.4 % / Redundancy: 9.9 % / Biso Wilson estimate: 73.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.046 / Rrim(I) all: 0.148 / Net I/σ(I): 14.9 / Num. measured all: 172129
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.85-310.41.8682559624620.5440.5951.9641.599.6
9.01-44.187.80.02750246460.9990.010.0295198

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GN1

6gn1


Resolution: 2.85→42.42 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 850 4.91 %RANDOM
Rwork0.203 16445 --
obs0.2042 17295 99.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 183.2 Å2 / Biso mean: 79.6962 Å2 / Biso min: 48.38 Å2
Refinement stepCycle: final / Resolution: 2.85→42.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2751 0 70 88 2909
Biso mean--85.23 71.02 -
Num. residues----356
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.85-3.030.3791270.33122689281699
3.03-3.260.34951570.27992647280498
3.26-3.590.27531510.235626812832100
3.59-4.110.24061300.18727412871100
4.11-5.180.16061440.16232762290699
5.18-42.420.2031410.18932925306699
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)
18.55752.74013.74165.99642.72139.2073-0.0257-0.3476-0.95920.27440.20660.07210.5959-0.2186-0.02230.42580.0132-0.02450.5732-0.12180.6955-8.6743-29.669331.4982
23.25182.95861.35536.3587-1.26512.3984-0.01240.1929-0.0732-0.10940.18930.7045-0.1543-0.6448-0.15210.36960.1246-0.1080.7813-0.11580.6713-10.541-20.188731.2446
31.98020.5473-0.16742.70330.59592.92990.03570.16680.0169-0.0976-0.09190.1553-0.2943-0.19520.06060.41970.1237-0.08530.49-0.01810.39374.455-5.229934.4772
40.52821.6575-0.88735.4632-1.32059.75550.1331-0.2960.674-0.2760.47470.664-1.749-0.4246-0.45121.09540.1543-0.07710.6558-0.03870.8074.934615.749445.073
54.4567-0.538-1.0625.02081.67374.8140.02460.90630.1362-0.88810.0977-0.0177-0.77060.0056-0.06870.62240.0311-0.06140.69450.09420.45759.19470.699919.9968
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 74 )A27 - 74
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 126 )A75 - 126
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 273 )A127 - 273
4X-RAY DIFFRACTION4chain 'A' and (resid 274 through 300 )A274 - 300
5X-RAY DIFFRACTION5chain 'A' and (resid 301 through 384 )A301 - 384

+
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