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- PDB-8vmf: Crystal structure of a transition-state mimic of the GSK-3/Axin c... -

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Basic information

Entry
Database: PDB / ID: 8vmf
TitleCrystal structure of a transition-state mimic of the GSK-3/Axin complex bound to a beta-catenin S45D 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 / 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 / myotube 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 / protein localization to microtubule / endodermal cell fate commitment / 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 / Formation of the nephric duct / endothelial tube morphogenesis / axial mesoderm formation / layer formation in cerebral cortex / dorsal/ventral axis specification / sympathetic ganglion development / negative regulation of cardiac muscle hypertrophy / establishment of blood-retinal barrier / positive regulation of myoblast proliferation / fungiform papilla formation / positive regulation of endothelial cell differentiation / presynaptic active zone cytoplasmic component / mesenchymal to epithelial transition / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / hindbrain development / lung epithelial cell differentiation / GLI3 is processed to GLI3R by the proteasome / positive regulation of determination of dorsal identity / positive regulation of skeletal muscle tissue development / ectoderm development / fascia adherens / regulation of protein localization to cell surface / embryonic foregut morphogenesis / positive regulation of stem cell differentiation / hair cell differentiation / negative regulation of TORC2 signaling / detection of muscle stretch / cellular response to indole-3-methanol / smooth muscle cell differentiation / positive regulation of odontoblast differentiation / mesenchymal cell proliferation involved in lung development / histone methyltransferase binding / alpha-catenin binding / regulation of calcium ion import / Germ layer formation at gastrulation / regulation of epithelial to mesenchymal transition / positive regulation of homotypic cell-cell adhesion
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 / ALUMINUM FLUORIDE / 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: 2.5 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: Axin-1
C: Catenin beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,03811
Polymers47,1673
Non-polymers8728
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-51 kcal/mol
Surface area17610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.251, 82.251, 280.354
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-611-

HOH

21A-722-

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: 41538.695 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: 2890.009 Da / Num. of mol.: 1 / Mutation: S45D
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 , 6 types, 139 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#6: 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
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.92 Å3/Da / Density % sol: 57.89 % / 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, 5 mM DTT, 200 uM ADP, 200 uM aluminum nitrate, 1.2 mM sodium fluoride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98401 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98401 Å / Relative weight: 1
ReflectionResolution: 2.5→39.07 Å / Num. obs: 19517 / % possible obs: 97 % / Redundancy: 4.4 % / Biso Wilson estimate: 54.32 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.233 / Rpim(I) all: 0.118 / Rrim(I) all: 0.263 / Net I/σ(I): 4.8
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.5 % / Rmerge(I) obs: 2.733 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 2182 / CC1/2: 0.188 / Rpim(I) all: 1.388 / Rrim(I) all: 2.935 / % possible all: 98.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSdata reduction
pointless1.9.33data scaling
Aimless0.5.12data 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: 2.5→39.07 Å / SU ML: 0.3783 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.9252
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2506 939 4.83 %
Rwork0.2091 18495 -
obs0.2101 19434 95.34 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.34 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2973 0 52 131 3156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00293167
X-RAY DIFFRACTIONf_angle_d0.53944319
X-RAY DIFFRACTIONf_chiral_restr0.0417488
X-RAY DIFFRACTIONf_plane_restr0.0045554
X-RAY DIFFRACTIONf_dihedral_angle_d11.30481165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.630.36911340.34582565X-RAY DIFFRACTION96.05
2.63-2.80.38391420.32072630X-RAY DIFFRACTION97.81
2.8-3.010.33121390.29492650X-RAY DIFFRACTION97.83
3.01-3.320.25481130.24322653X-RAY DIFFRACTION96.54
3.32-3.80.29211340.20422652X-RAY DIFFRACTION96.17
3.8-4.780.18931470.15392637X-RAY DIFFRACTION94.18
4.78-39.070.21641300.17462708X-RAY DIFFRACTION89.58
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)
16.81547181164-0.4523924799591.009623466586.1751677122-2.714170172163.50074811645-0.1484203244790.0432154674173-0.8557114106150.01294142648540.100246633965-0.5381093400740.1862226523810.0981713707634-0.006211214633250.555505192412-0.161098249557-0.06763513799870.731986260556-0.1309729255890.55597921220517.166-44.533-1.52
22.417480150840.192121154198-0.2899143388592.545389519190.2647565544924.586860956260.0251890664076-0.1387938615240.372108493284-0.008942801175780.05515236074920.0018561214223-0.4857959945890.201714345898-0.07317441309880.453421611731-0.03455319646890.06642502676810.4120838665690.03097217223310.4543835648124.5-29.78-21.403
32.00372792339-2.72868565828-0.6126848158558.919555732781.738890418466.711413792820.08780350720370.661957168243-0.176619702422-0.9901261556630.03321492688460.06482980296150.72445370144-0.148404962041-0.07257723347830.857675927556-0.1405951937690.04300788038160.4681309442660.08580923605380.4762682127894.8-43.993-44.203
40.575244555725-0.2078440949890.9162313393570.34389018874-0.5302250548131.8246744782-0.215613881831-1.4617724654-1.92005726630.8361272898650.8917400636481.142894228490.701140305442-0.175872488855-0.4189489660130.844249015220.08838521402680.2793352093321.180656162340.3946187482211.1090993060522.878-44.755-22.585
55.388084954090.288643662257-1.294713007973.527592417130.4857295476083.45290141326-0.2019377587380.68505582908-0.799369613511-0.4678336260290.0517145824466-0.3522852966050.296813213111-0.02189083270180.1583963590161.261458366150.266377967722-0.088255483751.52477661842-0.1344710469430.7229223235368.589-43.56-8.552
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 27:136 )A27 - 136
2X-RAY DIFFRACTION2( CHAIN A AND RESID 137:384 )A137 - 384
3X-RAY DIFFRACTION3( CHAIN B AND RESID 383:401 )B383 - 401
4X-RAY DIFFRACTION4( CHAIN C AND RESID 43:47 )C43 - 47
5X-RAY DIFFRACTION5( CHAIN A AND RESID 504:504 )A504

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