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- PDB-8vme: Crystal structure of the GSK-3/Axin complex bound to a phosphoryl... -

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Basic information

Entry
Database: PDB / ID: 8vme
TitleCrystal structure of the GSK-3/Axin complex bound to a phosphorylated beta-catenin T41A peptide
Components
  • Axin-1
  • Catenin beta-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 / TCF dependent signaling in response to WNT ...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 / TCF dependent signaling in response to WNT / Degradation of AXIN / myotube differentiation / positive regulation of heparan sulfate proteoglycan biosynthetic process / lung induction / positive regulation of branching involved in lung morphogenesis / cranial ganglion development / renal vesicle formation / renal inner medulla development / renal outer medulla development / nephron tubule formation / beta-catenin-ICAT complex / CDH11 homotypic and heterotypic interactions / genitalia morphogenesis / embryonic skeletal limb joint morphogenesis / canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / neural plate development / metanephros morphogenesis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / glial cell fate determination / Regulation of CDH19 Expression and Function / regulation of secondary heart field cardioblast proliferation / astrocyte-dopaminergic neuron signaling / oviduct development / beta-catenin-TCF7L2 complex / regulation of nephron tubule epithelial cell differentiation / regulation of timing of anagen / negative regulation of mitotic cell cycle, embryonic / Binding of TCF/LEF:CTNNB1 to target gene promoters / Transcriptional and post-translational regulation of MITF-M expression and activity / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / central nervous system vasculogenesis / positive regulation of cardiac muscle cell differentiation / regulation of centriole-centriole cohesion / head development / RUNX3 regulates WNT signaling / Degradation of beta-catenin by the destruction complex / regulation of centromeric sister chromatid cohesion / Regulation of CDH11 function / embryonic axis specification / Specification of the neural plate border / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / lens morphogenesis in camera-type eye / beta-catenin-TCF complex / endodermal cell fate commitment / protein localization to microtubule / acinar cell differentiation / dorsal root ganglion development / synaptic vesicle clustering / positive regulation of fibroblast growth factor receptor signaling pathway / proximal/distal pattern formation / neuron fate determination / layer formation in cerebral cortex / Formation of the nephric duct / positive regulation of myoblast proliferation / axial mesoderm formation / establishment of blood-retinal barrier / dorsal/ventral axis specification / sympathetic ganglion development / fungiform papilla formation / positive regulation of endothelial cell differentiation / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / presynaptic active zone cytoplasmic component / mesenchymal to epithelial transition / embryonic foregut morphogenesis / hindbrain development / lung epithelial cell differentiation / positive regulation of determination of dorsal identity / GLI3 is processed to GLI3R by the proteasome / positive regulation of skeletal muscle tissue development / ectoderm development / negative regulation of TORC2 signaling / positive regulation of stem cell differentiation / regulation of protein localization to cell surface / hair cell differentiation / cellular response to indole-3-methanol / detection of muscle stretch / mesenchymal stem cell differentiation / smooth muscle cell differentiation / positive regulation of odontoblast differentiation / negative regulation of cardiac muscle hypertrophy / endothelial tube morphogenesis / mesenchymal cell proliferation involved in lung development / midbrain dopaminergic neuron differentiation / positive regulation of homotypic cell-cell adhesion / histone methyltransferase binding / alpha-catenin binding / cranial skeletal system development / regulation of calcium ion import
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 / Beta-catenin / 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 / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold / 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 / Axin-1 / Catenin beta-1 / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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)T32 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,36813
Polymers47,3173
Non-polymers1,05110
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-65 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.257, 82.257, 280.990
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-656-

HOH

21A-663-

HOH

31A-665-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 41666.824 Da / Num. of mol.: 1
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

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Protein/peptide , 2 types, 2 molecules BC

#2: Protein/peptide Axin-1 / Axis inhibition protein 1 / Protein Fused


Mass: 2738.144 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Axin1, Axin, Fu / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O35625
#3: Protein/peptide Catenin beta-1 / Beta-catenin


Mass: 2911.952 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTNNB1, CTNNB, OK/SW-cl.35, PRO2286 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P35222

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Non-polymers , 5 types, 184 molecules

#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.93 Å3/Da / Density % sol: 58.01 % / Description: Flat plates
Crystal growTemperature: 277 K / Method: microdialysis / pH: 7.5
Details: 10% PEG35000, 20 mM Tris, pH 7.5, 300 mM sodium chloride, 5% glycerol, 10 mM magnesium chloride, 200 uM ATP, 5 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97949 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.3→39.47 Å / Num. obs: 26090 / % possible obs: 99.9 % / Redundancy: 35.5 % / Biso Wilson estimate: 59.57 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.026 / Rrim(I) all: 0.154 / Net I/σ(I): 17.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 21.8 % / Rmerge(I) obs: 5.635 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2435 / CC1/2: 0.399 / Rpim(I) all: 1.201 / Rrim(I) all: 5.768 / % possible all: 98.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSdata reduction
Aimless0.7.4data scaling
pointless1.11.21data scaling
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
Coot0.9.8.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4NM7

4nm7


Resolution: 2.3→39.47 Å / SU ML: 0.3359 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.0862
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2298 1297 5 %
obs0.1828 25928 99.53 %
Rwork-24632 -
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.36 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2997 0 66 174 3237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01043204
X-RAY DIFFRACTIONf_angle_d1.16394365
X-RAY DIFFRACTIONf_chiral_restr0.0593490
X-RAY DIFFRACTIONf_plane_restr0.0106558
X-RAY DIFFRACTIONf_dihedral_angle_d14.53971180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.390.37781380.35612565X-RAY DIFFRACTION96.4
2.39-2.50.34891600.29172669X-RAY DIFFRACTION99.72
2.5-2.630.30371390.22992670X-RAY DIFFRACTION99.86
2.63-2.80.26411410.21592689X-RAY DIFFRACTION99.89
2.8-3.010.26281420.22072715X-RAY DIFFRACTION99.93
3.01-3.320.29021200.20272748X-RAY DIFFRACTION100
3.32-3.80.22451390.17162763X-RAY DIFFRACTION99.93
3.8-4.780.18931580.14532798X-RAY DIFFRACTION100
4.78-39.470.20491600.16773015X-RAY DIFFRACTION99.94
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)
17.20241639203-0.07367500562640.4255588383245.89865182037-1.872164714575.22384605451-0.08689448930270.0184698279186-0.747136593903-0.1055124391880.0772252371101-0.5231857956190.3017556209450.300589637925-0.01854194940750.377166164431-0.110046328506-0.07345848778060.616110346008-0.09879494396940.52335664028917.314-44.398-1.48
22.2669562925-0.0742502863997-0.1240974590172.466185449760.4365900364394.836327741430.0384229479577-0.1725205294960.417271222444-0.1529083721860.0531235740629-0.0129089732729-0.5747531820340.249164040438-0.08482488810310.359755015083-0.03653566802510.07859319341660.3518846136080.01812597823080.5044993843184.512-29.628-21.411
32.83252033017-1.544102832351.772403468246.123427547211.173127713522.451120974980.7323104941110.884421445782-0.248147663999-1.0076986083-0.447820076862-0.2159100575960.452855419543-0.146668620459-0.2195435195270.8555750534290.01153346856230.06333825785290.6085768041540.03941845536570.6279730761044.676-43.928-44.002
42.51630558433-3.036692448254.231999826929.1697206318-3.038114351649.16536409413-0.209780774536-1.25667719903-2.332386551820.9019514818010.4159930771230.3079818761230.5771034217820.559042477685-0.3551840825810.9104383681310.2844705681440.01264376089431.378383028830.1604123430330.92801238013421.901-44.832-22.371
57.76657754444-3.08565804556-3.50375908945.015564365376.250811797687.868474902680.2938077562160.0273446088732-0.46195531972-0.5166842509350.6322662529780.4199297212330.4719083075280.716659681956-1.033391301280.8926273784680.15489296913-0.009308580809150.7713533918350.0426583694240.7096073675738.839-43.292-8.509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 25:136 )A25 - 136
2X-RAY DIFFRACTION2( CHAIN A AND RESID 137:384 )A137 - 384
3X-RAY DIFFRACTION3( CHAIN B AND RESID 382:401 )B382 - 401
4X-RAY DIFFRACTION4( CHAIN C AND RESID 42:47 )C42 - 47
5X-RAY DIFFRACTION5( CHAIN A AND RESID 401:401 )A401

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