[English] 日本語
Yorodumi
- PDB-4b7t: Glycogen Synthase Kinase 3 Beta complexed with Axin Peptide and L... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4b7t
TitleGlycogen Synthase Kinase 3 Beta complexed with Axin Peptide and Leucettine L4
Components
  • AXIN-1AXIN1
  • GLYCOGEN SYNTHASE KINASE-3 BETA
KeywordsTRANSFERASE/PEPTIDE / TRANSFERASE-PEPTIDE COMPLEX / TRANSFERASE / INSULIN PATHWAY / WNT SIGNALING PATHWAY / INHIBITOR
Function / homology
Function and homology information


armadillo repeat domain binding / head development / cell development / negative regulation of glycogen (starch) synthase activity / neuron projection organization / regulation of microtubule anchoring at centrosome / dorsal/ventral axis specification / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / negative regulation of type B pancreatic cell development ...armadillo repeat domain binding / head development / cell development / negative regulation of glycogen (starch) synthase activity / neuron projection organization / regulation of microtubule anchoring at centrosome / dorsal/ventral axis specification / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / negative regulation of type B pancreatic cell development / axial mesoderm formation / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / positive regulation of protein localization to centrosome / : / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of cilium assembly / post-anal tail morphogenesis / negative regulation of protein acetylation / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / epigenetic programming in the zygotic pronuclei / beta-catenin destruction complex / positive regulation of ubiquitin-dependent protein catabolic process / tau-protein kinase / regulation of microtubule-based process / CRMPs in Sema3A signaling / regulation of protein export from nucleus / heart valve development / 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 / Maturation of nucleoprotein / I-SMAD binding / negative regulation of protein metabolic process / cellular response to interleukin-3 / regulation of axon extension / Wnt signalosome / regulation of long-term synaptic potentiation / negative regulation of protein localization to nucleus / Disassembly of the destruction complex and recruitment of AXIN to the membrane / nucleocytoplasmic transport / Maturation of nucleoprotein / AKT phosphorylates targets in the cytosol / positive regulation of cell-matrix adhesion / negative regulation of calcineurin-NFAT signaling cascade / dopamine receptor signaling pathway / negative regulation of fat cell differentiation / regulation of dendrite morphogenesis / negative regulation of phosphoprotein phosphatase activity / regulation of axonogenesis / establishment of cell polarity / tau-protein kinase activity / glycogen metabolic process / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / ER overload response / regulation of neuron projection development / negative regulation of transcription elongation by RNA polymerase II / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / activation of protein kinase activity / Constitutive Signaling by AKT1 E17K in Cancer / dynactin binding / protein kinase A catalytic subunit binding / R-SMAD binding / ubiquitin-like ligase-substrate adaptor activity / NF-kappaB binding / canonical Wnt signaling pathway / Regulation of HSF1-mediated heat shock response / lateral plasma membrane / epithelial to mesenchymal transition / negative regulation of osteoblast differentiation / negative regulation of protein-containing complex assembly / signaling adaptor activity / regulation of microtubule cytoskeleton organization / positive regulation of autophagy / cytoplasmic microtubule organization / regulation of cellular response to heat / cellular response to retinoic acid / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / excitatory postsynaptic potential / presynaptic modulation of chemical synaptic transmission / positive regulation of protein export from nucleus / positive regulation of peptidyl-threonine phosphorylation / positive regulation of protein ubiquitination / TCF dependent signaling in response to WNT / Ubiquitin-dependent degradation of Cyclin D / cell periphery / hippocampus development / positive regulation of protein-containing complex assembly
Similarity search - Function
Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin ...Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / RGS, subdomain 1/3 / Glycogen synthase kinase 3, catalytic domain / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / Ubiquitin-like domain superfamily / 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-CWT / Axin-1 / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.772 Å
AuthorsOberholzer, A.E. / Pearl, L.H.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Selectivity, Cocrystal Structures, and Neuroprotective Properties of Leucettines, a Family of Protein Kinase Inhibitors Derived from the Marine Sponge Alkaloid Leucettamine B.
Authors: Tahtouh, T. / Elkins, J.M. / Filippakopoulos, P. / Soundararajan, M. / Burgy, G. / Durieu, E. / Cochet, C. / Schmid, R.S. / Lo, D.C. / Delhommel, F. / Oberholzer, A.E. / Pearl, L.H. / ...Authors: Tahtouh, T. / Elkins, J.M. / Filippakopoulos, P. / Soundararajan, M. / Burgy, G. / Durieu, E. / Cochet, C. / Schmid, R.S. / Lo, D.C. / Delhommel, F. / Oberholzer, A.E. / Pearl, L.H. / Carreaux, F. / Bazureau, J. / Knapp, S. / Meijer, L.
History
DepositionAug 22, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLYCOGEN SYNTHASE KINASE-3 BETA
B: AXIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2303
Polymers41,9422
Non-polymers2871
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-13.6 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.577, 81.577, 283.654
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein GLYCOGEN SYNTHASE KINASE-3 BETA / / GSK-3 BETA / SERINE/THREONINE-PROTEIN KINASE GSK3B


Mass: 39802.793 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-384
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: P49841, tau-protein kinase, non-specific serine/threonine protein kinase
#2: Protein/peptide AXIN-1 / AXIN1 / AXIS INHIBITION PROTEIN 1 / HAXIN


Mass: 2139.428 Da / Num. of mol.: 1 / Fragment: RESIDUES 383-400 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O15169
#3: Chemical ChemComp-CWT / (5Z)-5-(1,3-benzodioxol-5-ylmethylidene)-3-methyl-2-(propan-2-ylamino)imidazol-4-one / Leucettine L4


Mass: 287.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17N3O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.12 Å3/Da / Density % sol: 60.57 % / Description: NONE
Crystal growDetails: 0.1 M TRIS-HCL, PH 8.0, 0.15 M MGCL2, 15% (W/V) PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: OSMIC OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.77→29.99 Å / Num. obs: 14709 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 46.68 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.1
Reflection shellResolution: 2.77→2.94 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 7.1 / % possible all: 91.1

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O9U

1o9u


Resolution: 2.772→29.986 Å / SU ML: 0.36 / σ(F): 1.38 / Phase error: 20.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2353 747 5.1 %
Rwork0.1952 --
obs0.1973 14707 97.66 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.653 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.6648 Å20 Å20 Å2
2--5.6648 Å20 Å2
3----11.3297 Å2
Refinement stepCycle: LAST / Resolution: 2.772→29.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2946 0 21 53 3020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023042
X-RAY DIFFRACTIONf_angle_d0.5854139
X-RAY DIFFRACTIONf_dihedral_angle_d12.291147
X-RAY DIFFRACTIONf_chiral_restr0.039461
X-RAY DIFFRACTIONf_plane_restr0.003533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7722-2.9860.31111460.26262572X-RAY DIFFRACTION93
2.986-3.28620.28651460.23682764X-RAY DIFFRACTION99
3.2862-3.76090.24061470.20422794X-RAY DIFFRACTION99
3.7609-4.73540.20051480.16542822X-RAY DIFFRACTION98
4.7354-29.98790.21621600.17893008X-RAY DIFFRACTION98
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)
10.01540.0193-0.01120.0182-0.0020.0163-0.0115-0.07820.02660.0892-0.03950.09580.0086-0.0377-0.03160.1771-0.14570.24040.43410.01340.179-16.348245.04453.2618
20.02480.0080.02920.00180.00710.0508-0.03630.003-0.00740.0043-0.0580.00090.0146-0.024-0.00580.1532-0.04890.08230.31740.01080.2583-21.921142.1742-5.7381
30.0071-0.0081-0.02420.01480.00210.04310.0662-0.0625-0.02430.04760.0647-0.04190.0727-0.05540.1150.0879-0.0412-0.04930.1460.01750.1208-4.291234.3249-10.944
40.0047-0.0005-0.00290.0023-0.00110.0021-0.0007-0.0168-0.01410.0045-0.00330.0233-0.00710.0309-00.2465-0.0096-0.00430.42970.08030.3568-20.245337.4637-22.4653
5-0.0013-0.00080.0002-0.00390.00110.0033-0.0038-0.0374-0.0191-0.03550.02670.05180.0201-0.0051-0.00570.0152-0.071-0.1775-0.0149-0.0739-0.1687-4.814836.84-28.7195
60.0359-0.005-0.03440.00520.0070.0257-0.01340.0644-0.1418-0.1077-0.05260.01970.0874-0.0346-0.10390.2952-0.0505-0.19620.0412-0.0897-0.0275-2.983426.6109-31.7146
70.0303-0.01290.01040.0099-0.00230.0297-0.0339-0.0538-0.03340.0529-0.0287-0.03290.03360.04650.00650.3623-0.1241-0.17660.2310.18170.4839-5.652315.8579-7.9307
80.0070.00430.00560.00390.0030.00760.01770.0240.0093-0.02030.02190.02210.0063-0.00960.00390.2576-0.0285-0.04940.07010.05320.2699-5.742444.4938-44.527
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 35:89)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 90:125)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 126:198)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 199:218)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 219:273)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 274:344)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 345:384)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 383:400)

+
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