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- PDB-4djs: Structure of beta-catenin in complex with a stapled peptide inhibitor -

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Basic information

Entry
Database: PDB / ID: 4djs
TitleStructure of beta-catenin in complex with a stapled peptide inhibitor
Components
  • Catenin beta-1
  • stapled peptide RRWPQ(MK8)ILD(MK8)HVRRVWR
KeywordsSIGNALING PROTEIN/INHIBITOR / transcription regulation / SIGNALING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


CDH11 homotypic and heterotypic interactions / 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 / mesenchymal stem cell differentiation ...CDH11 homotypic and heterotypic interactions / 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 / mesenchymal stem cell differentiation / beta-catenin-ICAT complex / Regulation of CDH19 Expression and Function / metanephros morphogenesis / genitalia morphogenesis / embryonic skeletal limb joint morphogenesis / neural plate development / glial cell fate determination / regulation of secondary heart field cardioblast proliferation / astrocyte-dopaminergic neuron signaling / canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / oviduct development / beta-catenin-TCF7L2 complex / regulation of nephron tubule epithelial cell differentiation / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / regulation of timing of anagen / negative regulation of mitotic cell cycle, embryonic / Binding of TCF/LEF:CTNNB1 to target gene promoters / central nervous system vasculogenesis / RUNX3 regulates WNT signaling / regulation of centriole-centriole cohesion / Regulation of CDH11 function / regulation of centromeric sister chromatid cohesion / embryonic axis specification / Specification of the neural plate border / endodermal cell fate commitment / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / lens morphogenesis in camera-type eye / positive regulation of fibroblast growth factor receptor signaling pathway / mesenchymal cell proliferation involved in lung development / beta-catenin-TCF complex / dorsal root ganglion development / synaptic vesicle clustering / acinar cell differentiation / proximal/distal pattern formation / neuron fate determination / layer formation in cerebral cortex / dorsal/ventral axis specification / Formation of the nephric duct / positive regulation of endothelial cell differentiation / positive regulation of myoblast proliferation / establishment of blood-retinal barrier / fungiform papilla formation / sympathetic ganglion development / embryonic foregut morphogenesis / hindbrain development / lung epithelial cell differentiation / positive regulation of determination of dorsal identity / ectoderm development / positive regulation of skeletal muscle tissue development / regulation of calcium ion import / regulation of protein localization to cell surface / cellular response to indole-3-methanol / hair cell differentiation / endothelial tube morphogenesis / detection of muscle stretch / smooth muscle cell differentiation / presynaptic active zone cytoplasmic component / positive regulation of odontoblast differentiation / regulation of smooth muscle cell proliferation / cranial skeletal system development / midbrain dopaminergic neuron differentiation / histone methyltransferase binding / alpha-catenin binding / Germ layer formation at gastrulation / lung-associated mesenchyme development / establishment of blood-brain barrier / fascia adherens / negative regulation of oligodendrocyte differentiation / male genitalia development / apicolateral plasma membrane / flotillin complex / epithelial cell differentiation involved in prostate gland development / epithelial cell proliferation involved in prostate gland development / positive regulation of epithelial cell proliferation involved in prostate gland development / Formation of definitive endoderm / embryonic brain development / beta-catenin destruction complex / adherens junction assembly / oocyte development / Formation of axial mesoderm / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of protein sumoylation / 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 / catenin complex
Similarity search - Function
Beta-catenin / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Leucine-rich Repeat Variant / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.029 Å
AuthorsBowman, B.R. / Grossmann, T.N. / Yeh, J.T.-H. / Verdine, G.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Inhibition of oncogenic Wnt signaling through direct targeting of beta-catenin.
Authors: Grossmann, T.N. / Yeh, J.T. / Bowman, B.R. / Chu, Q. / Moellering, R.E. / Verdine, G.L.
History
DepositionFeb 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catenin beta-1
B: stapled peptide RRWPQ(MK8)ILD(MK8)HVRRVWR


Theoretical massNumber of molelcules
Total (without water)58,8322
Polymers58,8322
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-10 kcal/mol
Surface area22610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.060, 74.808, 135.714
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Catenin beta-1 / Beta-catenin


Mass: 56498.570 Da / Num. of mol.: 1 / Fragment: armadillo repeats 1-12 (UNP residues 148-665)
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 (E. coli) / References: UniProt: P35222
#2: Protein/peptide stapled peptide RRWPQ(MK8)ILD(MK8)HVRRVWR


Mass: 2333.827 Da / Num. of mol.: 1 / Source method: obtained synthetically

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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: 2.72 Å3/Da / Density % sol: 54.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 1.4-2.0 M sodium chloride, 100 mM Bis-Tris, 100 mM potassium phosphate monobasic, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2010
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.029→50.26 Å / Num. all: 12929 / Num. obs: 12929 / % possible obs: 99.9 %
Reflection shellHighest resolution: 3.029 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.1_357)refinement
CNSrefinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.029→50.26 Å / SU ML: 0.29 / σ(F): 0.11 / Phase error: 30.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2914 1210 9.95 %
Rwork0.2633 --
obs0.266 12159 93.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.094 Å2 / ksol: 0.334 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-40.2095 Å2-0 Å2-0 Å2
2---18.0463 Å20 Å2
3----22.1633 Å2
Refinement stepCycle: LAST / Resolution: 3.029→50.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4007 0 0 0 4007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024067
X-RAY DIFFRACTIONf_angle_d0.4875513
X-RAY DIFFRACTIONf_dihedral_angle_d11.0221520
X-RAY DIFFRACTIONf_chiral_restr0.032670
X-RAY DIFFRACTIONf_plane_restr0.002701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.029-3.15040.33181130.337986X-RAY DIFFRACTION78
3.1504-3.29370.33961180.31961100X-RAY DIFFRACTION87
3.2937-3.46740.35291330.30951159X-RAY DIFFRACTION91
3.4674-3.68450.31831260.27731206X-RAY DIFFRACTION93
3.6845-3.96890.31431390.26281250X-RAY DIFFRACTION96
3.9689-4.36810.26891380.24921255X-RAY DIFFRACTION98
4.3681-4.99970.2631440.23261304X-RAY DIFFRACTION99
4.9997-6.29720.30531450.27471306X-RAY DIFFRACTION98
6.2972-50.26720.23441540.22771383X-RAY DIFFRACTION99
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)
10.75540.10480.05171.0495-0.90952.4030.06840.44240.1678-0.3261-0.5065-0.0115-0.6875-0.3982-0.03450.6533-0.0567-0.01710.73040.09140.3518-11.218118.7504-90.3262
21.1183-1.2630.57681.774-1.18734.7313-0.07-0.1366-0.0427-0.11860.117-0.10070.1115-0.3084-0.02170.1416-0.0116-0.00390.2792-0.0030.3874-9.104214.4649-74.1386
3-1.21290.6051-0.3342.7876-0.67925.03790.1709-0.1041-0.24540.099-0.0541-0.0195-0.1176-0.4358-0.0080.11690.06160.01260.38060.09680.2996-9.636910.7068-46.529
42.3734-0.38680.881.4782-0.9931.5754-0.33810.0472-0.08210.51380.2773-0.0264-0.4039-0.13970.08330.4007-0.05690.0220.42210.05850.3694-7.61934.6017-26.3672
51.2576-0.82360.90072.2225-0.50081.0616-0.42820.132-0.03411.08490.50140.0623-0.2878-0.22030.02040.77370.0469-0.0690.34230.04670.436-0.3471-0.1264-17.3764
60.62330.6054-0.17925.3559-2.10650.9301-0.2273-0.5251-0.18552.87920.6254-1.5467-0.50250.70040.24871.2462-0.0388-0.65260.4603-0.14360.882510.38143.334-15.0264
70.22961.1527-0.03834.0107-0.15870.3151.4748-0.4876-0.84743.1155-0.5811-1.5102-0.36950.37310.19411.9138-0.0349-0.88660.5877-0.22151.055213.79646.1572-6.3697
81.56131.7215-0.57072.32940.91572.95960.0195-0.3235-0.48983.0768-0.4332-0.7969-2.69860.4833-0.43932.3857-0.2493-0.87150.29520.17650.831113.007612.0047-3.7548
91.6794-0.0638-0.87631.0796-1.1141.48610.1748-0.3150.93412.8664-1.40371.5317-1.79930.37810.01623.3847-0.2656-0.40550.5205-0.09910.51169.826520.7456-2.6184
101.32250.8251-0.18432.1351-0.50832.32921.1716-0.05010.32751.9718-0.9191.1616-1.86870.23120.10233.3934-0.4295-0.04150.7469-0.09460.78539.146922.57977.264
111.08991.18410.71234.1617-0.20321.95620.0979-0.6885-0.6201-1.17750.3233-0.55220.4849-0.4151-0.14460.6673-0.2223-0.12070.5917-0.00110.5146-15.11291.8041-65.2394
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( chain A and resid 148:166 )A148 - 166
2X-RAY DIFFRACTION2( chain A and resid 167:277 )A167 - 277
3X-RAY DIFFRACTION3( chain A and resid 278:388 )A278 - 388
4X-RAY DIFFRACTION4( chain A and resid 389:443 )A389 - 443
5X-RAY DIFFRACTION5( chain A and resid 444:490 )A444 - 490
6X-RAY DIFFRACTION6( chain A and resid 491:517 )A491 - 517
7X-RAY DIFFRACTION7( chain A and resid 518:549 )A518 - 549
8X-RAY DIFFRACTION8( chain A and resid 561:603 )A561 - 603
9X-RAY DIFFRACTION9( chain A and resid 604:621 )A604 - 621
10X-RAY DIFFRACTION10( chain A and resid 622:665 )A622 - 665
11X-RAY DIFFRACTION11( chain B and resid 2:16 )B2 - 16

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