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- PDB-8ru4: Crystal structure of Human Catenin Beta-1 in complex with stitche... -

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Basic information

Entry
Database: PDB / ID: 8ru4
TitleCrystal structure of Human Catenin Beta-1 in complex with stitched peptide inhibitor
Components
  • Axin-1
  • Catenin beta-1
KeywordsSIGNALING PROTEIN / Peptidometic inhibitor of Catenin Beta-1
Function / homology
Function and homology information


armadillo repeat domain binding / 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 ...armadillo repeat domain binding / 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 / head development / RUNX3 regulates WNT signaling / regulation of centriole-centriole cohesion / Regulation of CDH11 function / regulation of centromeric sister chromatid cohesion / embryonic axis specification / cell development / 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 / Formation of the nephric duct / dorsal/ventral axis specification / positive regulation of endothelial cell differentiation / positive regulation of myoblast proliferation / axial mesoderm formation / establishment of blood-retinal barrier / fungiform papilla formation / sympathetic ganglion development / embryonic foregut morphogenesis / hindbrain development / lung epithelial cell differentiation / ectoderm development / positive regulation of determination of dorsal identity / 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 / presynaptic active zone cytoplasmic component / smooth muscle cell differentiation / 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 / post-anal tail morphogenesis / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / embryonic brain development / beta-catenin destruction complex / adherens junction assembly / oocyte development / positive regulation of ubiquitin-dependent protein catabolic process / epigenetic programming in the zygotic pronuclei
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 / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin ...Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / RGS, subdomain 1/3 / Beta-catenin / 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
Similarity search - Domain/homology
alpha-D-glucopyranose / Axin-1 / Catenin beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsYeste Vazquez, A. / Klintrot, C.I.R. / Grossmann, T.N. / Hennig, S.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Structure-Based Design of Bicyclic Helical Peptides That Target the Oncogene beta-Catenin.
Authors: Yeste-Vazquez, A. / Paulussen, F.M. / Wendt, M. / Klintrot, R. / Schulte, C. / Wallraven, K. / van Gijzel, L. / Simeonov, B. / van der Gaag, M. / Gerber, A. / Maric, H.M. / Hennig, S. / Grossmann, T.N.
History
DepositionJan 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catenin beta-1
B: Catenin beta-1
C: Axin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,29617
Polymers115,4653
Non-polymers1,83114
Water5,909328
1
A: Catenin beta-1
C: Axin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3249
Polymers58,4812
Non-polymers8437
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-9 kcal/mol
Surface area22810 Å2
MethodPISA
2
B: Catenin beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9728
Polymers56,9841
Non-polymers9887
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-12 kcal/mol
Surface area23870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.567, 103.617, 187.923
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: SER / End label comp-ID: SER / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 153 - 663 / Label seq-ID: 11 - 521

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein / Protein/peptide / Sugars , 3 types, 10 molecules ABC

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


Mass: 56984.020 Da / Num. of mol.: 2
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
#2: Protein/peptide Axin-1 / Axis inhibition protein 1 / hAxin


Mass: 1496.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O15169
#3: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 335 molecules

#4: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 100 mM TRIS pH 8.75, 2%(w/v) PEG-6000, cryoprotected in 30% (w/v) Glucose.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9212 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9212 Å / Relative weight: 1
ReflectionResolution: 2.129→93.961 Å / Num. obs: 51113 / % possible obs: 94.7 % / Observed criterion σ(I): 1 / Redundancy: 13.7 % / CC1/2: 0.999 / Rpim(I) all: 0.036 / Net I/σ(I): 11.9
Reflection shellResolution: 2.129→2.31 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2551 / CC1/2: 0.816 / Rpim(I) all: 0.319 / % possible all: 64.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
GDAdata collection
DIALSdata reduction
STARANISOdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→93.961 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2 / WRfactor Rwork: 0.167 / SU B: 7.764 / SU ML: 0.183 / Average fsc free: 0.9551 / Average fsc work: 0.9681 / Cross valid method: FREE R-VALUE / ESU R: 0.348 / ESU R Free: 0.238
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2403 2502 4.895 %
Rwork0.2011 48608 -
all0.203 --
obs-51110 72.073 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.028 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å2-0 Å2
2---0.827 Å20 Å2
3---0.257 Å2
Refinement stepCycle: LAST / Resolution: 2.13→93.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7696 0 119 328 8143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0127958
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167897
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.83610809
X-RAY DIFFRACTIONr_angle_other_deg0.4371.75718090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.01951052
X-RAY DIFFRACTIONr_dihedral_angle_other_1_deg10.52028
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.207553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.310.1021379
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.21310305
X-RAY DIFFRACTIONr_chiral_restr0.0630.21345
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029222
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021684
X-RAY DIFFRACTIONr_nbd_refined0.1970.21805
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.26819
X-RAY DIFFRACTIONr_nbtor_refined0.1580.24021
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0680.24336
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0010.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0850.211
X-RAY DIFFRACTIONr_nbd_other0.1390.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1440.27
X-RAY DIFFRACTIONr_mcbond_it7.3544.6054089
X-RAY DIFFRACTIONr_mcbond_other7.3454.6044088
X-RAY DIFFRACTIONr_mcangle_it10.1568.2425097
X-RAY DIFFRACTIONr_mcangle_other10.1588.2435097
X-RAY DIFFRACTIONr_scbond_it8.6225.1923869
X-RAY DIFFRACTIONr_scbond_other8.6175.1933867
X-RAY DIFFRACTIONr_scangle_it12.0419.3035712
X-RAY DIFFRACTIONr_scangle_other12.049.3045713
X-RAY DIFFRACTIONr_lrange_it14.55855.00133926
X-RAY DIFFRACTIONr_lrange_other14.57755.00533766
X-RAY DIFFRACTIONr_ncsr_local_group_10.1110.0515375
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.111220.05008
12AX-RAY DIFFRACTIONLocal ncs0.111220.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.13-2.1850.27670.278950.27847240.9390.9362.15920.259
2.185-2.2450.345450.3067440.30850660.920.92315.57440.291
2.245-2.310.306710.28415930.28549950.930.93933.31330.265
2.31-2.3810.3231090.27420380.27747550.9260.94645.15250.253
2.381-2.4590.2631170.25725540.25746490.9520.95357.45320.233
2.459-2.5460.2691480.24528370.24645370.950.9665.79240.216
2.546-2.6420.2711790.23532140.23743470.9470.96278.05380.201
2.642-2.7490.311980.24735820.25141970.9330.95890.06430.204
2.749-2.8710.2782060.23337740.23540450.950.96398.39310.19
2.871-3.0110.2721890.21936740.22238630.9530.9681000.176
3.011-3.1740.2591690.2135110.21236800.9540.9721000.17
3.174-3.3670.2591720.20733250.20934970.9550.9741000.175
3.367-3.5990.2651470.19931580.20233050.9590.9771000.169
3.599-3.8860.2251520.17629000.17930520.970.9831000.148
3.886-4.2570.1921360.15427170.15628530.9780.9861000.133
4.257-4.7580.1631110.14124760.14125870.9840.9891000.125
4.758-5.4920.1851160.17221970.17323130.9830.9841000.15
5.492-6.720.2951020.2118560.21419580.9550.9751000.179
6.72-9.4790.185920.16314720.16515640.9810.9861000.159
9.479-93.9610.256360.2838910.2829270.970.9521000.283

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