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- PDB-8vmg: Crystal structure of GSK-3 26-383 bound to Axin 383-435 -

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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 / beta-catenin destruction complex assembly / negative regulation of protein localization to centrosome / 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 / beta-catenin destruction complex assembly / negative regulation of protein localization to centrosome / 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 / 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 / myotube differentiation / head development / Degradation of beta-catenin by the destruction complex / cell development / protein localization to microtubule / axial mesoderm formation / dorsal/ventral axis specification / negative regulation of cardiac muscle hypertrophy / 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 / positive regulation of cilium assembly / autosome genomic imprinting / post-anal tail morphogenesis / beta-catenin destruction complex / tau-protein kinase / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / meiosis I / regulation of protein export from nucleus / myoblast fusion / 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 / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / cellular response to interleukin-3 / I-SMAD binding / positive regulation of ubiquitin-dependent protein catabolic process / epigenetic programming in the zygotic pronuclei / phosphorylation / regulation of microtubule-based process / Wnt signalosome / axon extension / regulation of long-term synaptic potentiation / negative regulation of TOR signaling / Disassembly of the destruction complex and recruitment of AXIN to the membrane / meiotic spindle / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of protein metabolic process / nucleocytoplasmic transport / tau-protein kinase activity / negative regulation of epithelial to mesenchymal transition / cellular response to glucocorticoid stimulus / cellular response to hepatocyte growth factor stimulus / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / glycogen metabolic process / ER overload response / negative regulation of fat cell differentiation / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / regulation of neuron projection development / fat cell differentiation / dynein complex binding / R-SMAD binding / negative regulation of transcription elongation by RNA polymerase II / epithelial to mesenchymal transition / lateral plasma membrane / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / 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 / cytoplasmic microtubule organization / signaling adaptor activity / extrinsic apoptotic signaling pathway in absence of ligand / cytoskeleton organization / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of autophagy / axonogenesis / protein serine/threonine kinase binding / protein export from nucleus / lipopolysaccharide-mediated signaling pathway / animal organ morphogenesis / positive regulation of protein export from nucleus / dendritic shaft / protein serine/threonine kinase activator activity / positive regulation of protein ubiquitination / cell periphery / TCF dependent signaling in response to WNT
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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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

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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

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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

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