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- PDB-7uwi: Structure of beta-catenin in complex with FP01567, a Helicon Poly... -

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Basic information

Entry
Database: PDB / ID: 7uwi
TitleStructure of beta-catenin in complex with FP01567, a Helicon Polypeptide
Components
  • Catenin beta-1
  • Helicon Polypeptide FP01567
KeywordsTRANSCRIPTION / Inhibitor / complex / stapled
Function / homology
Function and homology information


CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / 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 ...CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / 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 / 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 / negative regulation of mitotic cell cycle, embryonic / 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 / 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 / endodermal cell fate commitment / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / positive regulation of fibroblast growth factor receptor signaling pathway / beta-catenin-TCF complex / lens morphogenesis in camera-type eye / dorsal root ganglion development / synaptic vesicle clustering / acinar cell differentiation / dorsal/ventral axis specification / proximal/distal pattern formation / neuron fate determination / layer formation in cerebral cortex / positive regulation of myoblast proliferation / positive regulation of endothelial cell differentiation / sympathetic ganglion development / establishment of blood-retinal barrier / fungiform papilla formation / lung epithelial cell differentiation / embryonic foregut morphogenesis / hindbrain development / regulation of calcium ion import / positive regulation of determination of dorsal identity / positive regulation of skeletal muscle tissue development / ectoderm development / positive regulation of odontoblast differentiation / cranial skeletal system development / endothelial tube morphogenesis / regulation of protein localization to cell surface / hair cell differentiation / mesenchymal cell proliferation involved in lung development / detection of muscle stretch / smooth muscle cell differentiation / histone methyltransferase binding / midbrain dopaminergic neuron differentiation / presynaptic active zone cytoplasmic component / alpha-catenin binding / cellular response to indole-3-methanol / flotillin complex / Germ layer formation at gastrulation / establishment of blood-brain barrier / male genitalia development / negative regulation of oligodendrocyte differentiation / apicolateral plasma membrane / fascia adherens / epithelial cell proliferation involved in prostate gland development / embryonic brain development / Formation of definitive endoderm / epithelial cell differentiation involved in prostate gland development / positive regulation of epithelial cell proliferation involved in prostate gland development / regulation of smooth muscle cell proliferation / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / oocyte development / beta-catenin destruction complex / lung-associated mesenchyme development / Formation of axial mesoderm / negative regulation of protein sumoylation / adherens junction assembly / embryonic heart tube development / 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 / Adherens junctions interactions / catenin complex
Similarity search - Function
Beta-catenin / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
PHOSPHATE ION / N,N'-(1,4-phenylene)diacetamide / Catenin beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsBrennan, M. / Agarwal, S. / Thomson, T. / Wahl, S. / Ramirez, J. / Verdine, G. / McGee, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: De novo mapping of alpha-helix recognition sites on protein surfaces using unbiased libraries.
Authors: Li, K. / Tokareva, O.S. / Thomson, T.M. / Wahl, S.C.T. / Travaline, T.L. / Ramirez, J.D. / Choudary, S.K. / Agarwal, S. / Walkup 4th, W.G. / Olsen, T.J. / Brennan, M.J. / Verdine, G.L. / McGee, J.H.
History
DepositionMay 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catenin beta-1
F: Helicon Polypeptide FP01567
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,39310
Polymers58,5532
Non-polymers8408
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-21 kcal/mol
Surface area22580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.680, 91.810, 113.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AF

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


Mass: 56812.863 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 (E. coli) / References: UniProt: P35222
#2: Protein/peptide Helicon Polypeptide FP01567


Mass: 1740.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Wahl stapled peptide / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 68 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical ChemComp-WHL / N,N'-(1,4-phenylene)diacetamide


Mass: 192.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Sodium phosphate monobasic monohydrate, 0.1 M Potassium phosphate monobasic, 0.1 M MES monohydrate pH 6.5, 2.0 M Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: May 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.32→71.34 Å / Num. obs: 23082 / % possible obs: 99.68 % / Redundancy: 7.1 % / Biso Wilson estimate: 51.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.115 / Net I/σ(I): 8.6
Reflection shellResolution: 2.32→2.403 Å / Num. unique obs: 2271 / CC1/2: 0.665

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Processing

Software
NameVersionClassification
PHENIX1.20_4444refinement
PDB_EXTRACT3.27data extraction
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QZ7

1qz7


Resolution: 2.32→71.34 Å / SU ML: 0.3894 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.7414
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2775 1126 4.88 %RANDOM
Rwork0.2357 21953 --
obs0.2378 23079 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.98 Å2
Refinement stepCycle: LAST / Resolution: 2.32→71.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3952 0 56 60 4068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00264063
X-RAY DIFFRACTIONf_angle_d0.54525505
X-RAY DIFFRACTIONf_chiral_restr0.0365666
X-RAY DIFFRACTIONf_plane_restr0.0044699
X-RAY DIFFRACTIONf_dihedral_angle_d16.36441501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.430.39311380.35342690X-RAY DIFFRACTION99.61
2.43-2.550.40021210.34542709X-RAY DIFFRACTION99.68
2.55-2.710.39641390.32662697X-RAY DIFFRACTION99.58
2.71-2.920.35051440.30612712X-RAY DIFFRACTION99.69
2.92-3.220.32111520.26792711X-RAY DIFFRACTION99.72
3.22-3.680.27821420.24892734X-RAY DIFFRACTION99.58
3.68-4.640.24081300.1892789X-RAY DIFFRACTION99.73
4.64-71.340.22551600.19732911X-RAY DIFFRACTION99.87
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)
18.28012668169-3.7195305606-3.733347916553.939530619221.626492250582.357269638250.1747392324410.1382877522030.150054690030.0503628460397-0.02736657082070.234932190121-0.174054224346-0.107978302184-0.1355244672810.504758070723-0.0517149848202-0.09566506275040.4016615501820.06934992434520.236896228494-29.755116433129.1147853682-12.3584749176
21.42851905393-2.99588352619-0.1742475416679.15379747290.382122564880.67071035461-0.0116172960439-0.0877797371134-0.2005027465550.3218607792630.007139441812420.01477963483460.169994733867-0.01671749075070.01113538653370.342542274098-0.0489298777778-0.01554136860990.4289953481380.01266314598810.34297739496910.1205001465-8.35907374193-16.1419249901
32.00290724468-4.755478360095.063053173849.58752552288-2.115283836585.34992623409-0.736916905859-0.09658655496412.188963640851.99580582612-0.395094207385-2.18403258888-0.9594446822380.7956696986791.134326329330.802047733444-0.0833381261532-0.1022735332350.6508267284730.007613330241230.730281775202-18.296468024135.1786373047-10.7440272145
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 147 through 374 )AA147 - 3741 - 228
22chain 'A' and (resid 375 through 663 )AA375 - 663229 - 505
33chain 'F' and (resid 3 through 15 )FB3 - 151 - 13

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