[English] 日本語
Yorodumi
- PDB-8vmg: Crystal structure of GSK-3 26-383 bound to Axin 383-435 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vmg
TitleCrystal structure of GSK-3 26-383 bound to Axin 383-435
Components
  • Axin-1
  • Glycogen synthase kinase-3 beta
KeywordsTRANSFERASE/SIGNALING PROTEIN / GSK-3 / kinase / TRANSFERASE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


Regulation of HSF1-mediated heat shock response / negative regulation of protein localization to centrosome / beta-catenin destruction complex assembly / B-WICH complex positively regulates rRNA expression / negative regulation of neuron maturation / Beta-catenin phosphorylation cascade / CRMPs in Sema3A signaling / re-entry into mitotic cell cycle / Disassembly of the destruction complex and recruitment of AXIN to the membrane / armadillo repeat domain binding ...Regulation of HSF1-mediated heat shock response / negative regulation of protein localization to centrosome / beta-catenin destruction complex assembly / B-WICH complex positively regulates rRNA expression / negative regulation of neuron maturation / Beta-catenin phosphorylation cascade / CRMPs in Sema3A signaling / re-entry into mitotic cell cycle / Disassembly of the destruction complex and recruitment of AXIN to the membrane / armadillo repeat domain binding / myotube differentiation / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of cardiac muscle cell differentiation / head development / Degradation of beta-catenin by the destruction complex / cell development / protein localization to microtubule / axial mesoderm formation / dorsal/ventral axis specification / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / GLI3 is processed to GLI3R by the proteasome / negative regulation of TORC2 signaling / positive regulation of stem cell differentiation / negative regulation of cardiac muscle hypertrophy / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / autosome genomic imprinting / activation of protein kinase activity / positive regulation of cilium assembly / post-anal tail morphogenesis / 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 / tau-protein kinase / meiosis I / regulation of microtubule-based process / myoblast fusion / regulation of protein export from nucleus / epigenetic programming in the zygotic pronuclei / 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 / I-SMAD binding / cellular response to interleukin-3 / positive regulation of ubiquitin-dependent protein catabolic process / axon extension / regulation of long-term synaptic potentiation / Wnt signalosome / negative regulation of TOR signaling / meiotic spindle / Disassembly of the destruction complex and recruitment of AXIN to the membrane / cellular response to glucocorticoid stimulus / negative regulation of calcineurin-NFAT signaling cascade / nucleocytoplasmic transport / negative regulation of protein metabolic process / negative regulation of epithelial to mesenchymal transition / tau-protein kinase activity / phosphorylation / cellular response to hepatocyte growth factor stimulus / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / ER overload response / glycogen metabolic process / negative regulation of fat cell differentiation / regulation of neuron projection development / positive regulation of transforming growth factor beta receptor signaling pathway / dynein complex binding / SMAD binding / fat cell differentiation / R-SMAD binding / negative regulation of transcription elongation by RNA polymerase II / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / epithelial to mesenchymal transition / lateral plasma membrane / canonical Wnt signaling pathway / positive regulation of axon extension / ubiquitin-like ligase-substrate adaptor activity / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway / positive regulation of autophagy / signaling adaptor activity / protein serine/threonine kinase binding / cytoplasmic microtubule organization / cytoskeleton organization / axonogenesis / protein export from nucleus / dendritic shaft / positive regulation of protein export from nucleus / positive regulation of protein ubiquitination / animal organ morphogenesis / cell periphery / TCF dependent signaling in response to WNT / stem cell differentiation / phosphatidylinositol 3-kinase/protein kinase B signal transduction
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 / RGS, subdomain 1/3 / DIX domain superfamily / DIX domain / DIX domain profile. ...Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / RGS, subdomain 1/3 / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / Glycogen synthase kinase 3, catalytic domain / : / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / Ubiquitin-like domain superfamily / 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
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / NITRATE ION / Axin-1 / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsEnos, M.D. / Gavagan, M. / Jameson, N. / Zalatan, J.G. / Weis, W.I.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131747 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM119156 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM007276 United States
CitationJournal: Sci.Signal. / Year: 2024
Title: Structural and functional effects of phosphopriming and scaffolding in the kinase GSK-3 beta.
Authors: Enos, M.D. / Gavagan, M. / Jameson, N. / Zalatan, J.G. / Weis, W.I.
History
DepositionJan 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycogen synthase kinase-3 beta
B: Glycogen synthase kinase-3 beta
C: Axin-1
D: Axin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,72082
Polymers96,3924
Non-polymers5,32878
Water2,846158
1
A: Glycogen synthase kinase-3 beta
C: Axin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,67450
Polymers48,1962
Non-polymers3,47848
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-173 kcal/mol
Surface area19880 Å2
MethodPISA
2
B: Glycogen synthase kinase-3 beta
D: Axin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,04632
Polymers48,1962
Non-polymers1,85030
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-119 kcal/mol
Surface area18540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.585, 195.585, 152.204
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

-
Components

-
Protein , 2 types, 4 molecules ABCD

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


Mass: 41538.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gsk3b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9WV60, tau-protein kinase, non-specific serine/threonine protein kinase
#2: Protein Axin-1 / Axis inhibition protein 1 / hAxin


Mass: 6657.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AXIN1, AXIN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O15169

-
Non-polymers , 9 types, 236 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: NO3
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.36 Å3/Da / Density % sol: 71.8 % / Description: Hexagonal bipyramidal
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM MES, pH 5.5, 1.9 M ammonium sulfate, 200 mM sodium chloride, cryoprotectant: 25% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.45→39.76 Å / Num. obs: 63244 / % possible obs: 99.9 % / Redundancy: 41.1 % / Biso Wilson estimate: 66.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.222 / Rpim(I) all: 0.035 / Rrim(I) all: 0.225 / Net I/σ(I): 15.9
Reflection shellResolution: 2.45→2.51 Å / Redundancy: 42.2 % / Rmerge(I) obs: 8.11 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4331 / CC1/2: 0.414 / Rpim(I) all: 1.258 / Rrim(I) all: 8.208 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSdata reduction
pointless1.12.2data scaling
Aimless0.7.4data scaling
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
Coot0.9.8.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4NM0

4nm0


Resolution: 2.45→39.76 Å / SU ML: 0.4315 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6462
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2301 1997 3.16 %
Rwork0.1947 61158 -
obs0.1953 63154 99.94 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.85 Å2
Refinement stepCycle: LAST / Resolution: 2.45→39.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6116 0 312 158 6586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616602
X-RAY DIFFRACTIONf_angle_d0.84138925
X-RAY DIFFRACTIONf_chiral_restr0.0466990
X-RAY DIFFRACTIONf_plane_restr0.00751141
X-RAY DIFFRACTIONf_dihedral_angle_d13.2372460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.510.49281380.44564269X-RAY DIFFRACTION99.44
2.51-2.580.38911410.36264305X-RAY DIFFRACTION99.84
2.58-2.660.37311400.32034291X-RAY DIFFRACTION99.98
2.66-2.740.32871410.27854312X-RAY DIFFRACTION99.98
2.74-2.840.30891410.24024309X-RAY DIFFRACTION100
2.84-2.950.26111410.23844325X-RAY DIFFRACTION100
2.95-3.090.30181410.25124327X-RAY DIFFRACTION100
3.09-3.250.29751420.23434349X-RAY DIFFRACTION100
3.25-3.450.25571420.20424343X-RAY DIFFRACTION100
3.45-3.720.22881430.18174367X-RAY DIFFRACTION100
3.72-4.090.19181430.16784380X-RAY DIFFRACTION100
4.09-4.680.15681440.14644421X-RAY DIFFRACTION100
4.68-5.90.21151470.16714471X-RAY DIFFRACTION100
5.9-39.760.20891530.17524689X-RAY DIFFRACTION99.92
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)
15.329357397591.89557138904-1.134714771156.35893155912-1.484653060183.798180123180.207150441686-0.228314817965-0.1445839587190.2982807443940.007184136764960.439573742165-0.191132777612-0.0702902472889-0.2228811348930.704056051387-0.003726685133340.02062137437060.3772547003970.08369142877460.406814598169-98.43810.333-5.333
21.556727201520.416237355022-0.08003113257961.64568301044-0.0224721708762.203641905510.122032091025-0.0467942179504-0.0847823100520.154253789610.00951514701015-0.0727996409176-0.229082534020.204821543899-0.1227761101120.558567857908-0.06795996540360.007608480265510.353071625515-0.04119384827970.413058479292-81.52125.184-23.771
36.500528468914.78716853446-0.09360558330593.82755526747-0.4632968148532.799426992070.02598722493540.73911680778-0.89732372540.04596044112020.125075721517-0.5225499384650.1361264664520.0845275175826-0.1874491047860.678804623983-0.207394343349-0.06848975041550.813683466816-0.1466330351480.706460944371-39.80861.968-28.806
44.635345894571.578696141530.9065565754383.123681312960.2845905046011.626534070910.263201011549-0.1533153367490.1746300786260.162190176321-0.08290876318920.0852073382117-0.1963584013540.197884411652-0.1950278556370.684077635183-0.1870237614370.1119558083020.505750334632-0.1427465336440.530727724928-65.47950.788-27.794
57.42951959806-3.547990734213.277756652876.68018989428-5.181696968378.803106516710.3139905973520.5916015495290.13399478418-0.9106752131770.1469054982140.2012408452180.0595381862724-0.0428231090136-0.4158346680210.685599420802-0.05213931409910.06846153517060.465974359378-0.1157760525660.451919471141-84.19619.944-51.78
68.84237797187-0.816114267371-0.7118863818145.6860735568-0.6916910740264.708689425850.2439914409050.4223208883311.56487470309-0.913688062576-0.1780995493031.25091199928-1.29157239090.0543673319763-0.1232628797841.010480052730.0560407111949-0.01639773363930.7291368457940.02774044857471.73559504764-84.33967.83-34.813
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 26:136 )A26 - 136
2X-RAY DIFFRACTION2( CHAIN A AND RESID 137:384 )A137 - 384
3X-RAY DIFFRACTION3( CHAIN B AND RESID 35:136 )B35 - 136
4X-RAY DIFFRACTION4( CHAIN B AND RESID 137:384 )B137 - 384
5X-RAY DIFFRACTION5( CHAIN C AND ( RESID 382:416 OR RESID 502:504 ) )C382 - 416
6X-RAY DIFFRACTION5( CHAIN C AND ( RESID 382:416 OR RESID 502:504 ) )C502 - 504
7X-RAY DIFFRACTION6( CHAIN D AND RESID 378:411 ) OR ( CHAIN B AND RESID 420:420 )D378 - 411
8X-RAY DIFFRACTION6( CHAIN D AND RESID 378:411 ) OR ( CHAIN B AND RESID 420:420 )B420

+
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