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- PDB-7ar4: Crystal structure of beta-catenin in complex with cyclic peptide ... -

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Basic information

Entry
Database: PDB / ID: 7ar4
TitleCrystal structure of beta-catenin in complex with cyclic peptide inhibitor
Components
  • Cadherin-1
  • Catenin beta-1
KeywordsSIGNALING PROTEIN / Wnt signaling / Peptide Inhibitor / Protein-Peptide Interaction
Function / homology
Function and homology information


uterine epithelium development / Apoptotic cleavage of cell adhesion proteins / 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 ...uterine epithelium development / Apoptotic cleavage of cell adhesion proteins / 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 / regulation of branching involved in salivary gland morphogenesis / Binding of TCF/LEF:CTNNB1 to target gene promoters / central nervous system vasculogenesis / salivary gland cavitation / RUNX3 regulates WNT signaling / regulation of centriole-centriole cohesion / Regulation of CDH11 function / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / RHO GTPases activate IQGAPs / regulation of centromeric sister chromatid cohesion / Adherens junctions interactions / Specification of the neural plate border / embryonic axis specification / endodermal cell fate commitment / Degradation of the extracellular matrix / positive regulation of fibroblast growth factor receptor signaling pathway / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / beta-catenin-TCF complex / lens morphogenesis in camera-type eye / dorsal root ganglion development / synaptic vesicle clustering / positive regulation of cell-cell adhesion / acinar cell differentiation / Integrin cell surface interactions / dorsal/ventral axis specification / proximal/distal pattern formation / neuron fate determination / lateral loop / regulation of neuron migration / Formation of the nephric duct / layer formation in cerebral cortex / positive regulation of myoblast proliferation / positive regulation of endothelial cell differentiation / establishment of blood-retinal barrier / sympathetic ganglion development / fungiform papilla formation / lung epithelial cell differentiation / embryonic foregut morphogenesis / hindbrain development / regulation of calcium ion import / positive regulation of skeletal muscle tissue development / positive regulation of determination of dorsal identity / ectoderm development / positive regulation of odontoblast differentiation / negative regulation of axon extension / cell-cell adhesion mediated by cadherin / cranial skeletal system development / endothelial tube morphogenesis / regulation of protein localization to cell surface / hair cell differentiation / cellular response to indole-3-methanol / mesenchymal cell proliferation involved in lung development / presynaptic active zone cytoplasmic component / trophectodermal cell differentiation / detection of muscle stretch / smooth muscle cell differentiation / histone methyltransferase binding / midbrain dopaminergic neuron differentiation / alpha-catenin binding / epithelial cell morphogenesis / flotillin complex / establishment of blood-brain barrier / Germ layer formation at gastrulation / Schmidt-Lanterman incisure / male genitalia development / negative regulation of oligodendrocyte differentiation / fascia adherens / bicellular tight junction assembly / epithelial cell proliferation involved in prostate gland development / apicolateral plasma membrane / embryonic brain development
Similarity search - Function
Beta-catenin / Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherin / Cadherin conserved site / Cadherin domain signature. ...Beta-catenin / Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / 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
Cadherin-1 / Catenin beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWendt, M. / Pearce, N.M. / Grossmann, T.N. / Hennig, S.
Funding support1items
OrganizationGrant numberCountry
European Research Council (ERC)
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Bicyclic beta-Sheet Mimetics that Target the Transcriptional Coactivator beta-Catenin and Inhibit Wnt Signaling.
Authors: Wendt, M. / Bellavita, R. / Gerber, A. / Efrem, N.L. / van Ramshorst, T. / Pearce, N.M. / Davey, P.R.J. / Everard, I. / Vazquez-Chantada, M. / Chiarparin, E. / Grieco, P. / Hennig, S. / Grossmann, T.N.
History
DepositionOct 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jun 16, 2021Group: Atomic model / Database references / Category: atom_site / citation / citation_author
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 2.1Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Catenin beta-1
PaP: Cadherin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4014
Polymers60,1282
Non-polymers2742
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-12 kcal/mol
Surface area22670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.380, 85.620, 142.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 58412.656 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 Cadherin-1 / ARC-1 / Epithelial cadherin / E-cadherin / Uvomorulin


Mass: 1714.936 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P09803
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
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: 3.62 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES, 4% PEG6000, 20 mM TRIS, 150 mM NaCl, 0.5 % Glycerol, 2 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979507 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979507 Å / Relative weight: 1
ReflectionResolution: 2.6→85.62 Å / Num. obs: 27652 / % possible obs: 100 % / Redundancy: 13.36 % / CC1/2: 0.999 / Rrim(I) all: 0.171 / Net I/σ(I): 12.83
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 14.23 % / Mean I/σ(I) obs: 1.11 / Num. unique obs: 2886 / CC1/2: 0.584 / Rrim(I) all: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JDH

1jdh


Resolution: 2.6→85.62 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 25.261 / SU ML: 0.227 / Cross valid method: FREE R-VALUE / ESU R: 0.344 / ESU R Free: 0.253
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2419 1380 5.001 %
Rwork0.2026 26216 -
all0.205 --
obs-27596 99.975 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 72.408 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20 Å20 Å2
2--1.54 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.6→85.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4017 0 16 46 4079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134095
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173994
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.6375560
X-RAY DIFFRACTIONr_angle_other_deg1.2241.5729237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6355523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32622195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97315727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9361530
X-RAY DIFFRACTIONr_chiral_restr0.0620.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024542
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02777
X-RAY DIFFRACTIONr_nbd_refined0.2030.21009
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.23854
X-RAY DIFFRACTIONr_nbtor_refined0.1470.21996
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21942
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.265
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1650.210
X-RAY DIFFRACTIONr_nbd_other0.2010.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.240.24
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0970.21
X-RAY DIFFRACTIONr_mcbond_it1.3125.6842107
X-RAY DIFFRACTIONr_mcbond_other1.3125.6862108
X-RAY DIFFRACTIONr_mcangle_it2.2018.5242632
X-RAY DIFFRACTIONr_mcangle_other2.1818.522630
X-RAY DIFFRACTIONr_scbond_it1.4165.9751988
X-RAY DIFFRACTIONr_scbond_other1.4165.9771989
X-RAY DIFFRACTIONr_scangle_it2.4068.8672927
X-RAY DIFFRACTIONr_scangle_other2.4058.8682928
X-RAY DIFFRACTIONr_lrange_it4.46369.7744536
X-RAY DIFFRACTIONr_lrange_other4.46669.784536
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
2.6-2.6680.371990.35818880.35919870.560.5861000.351
2.668-2.7410.333980.32318630.32419610.7350.7271000.309
2.741-2.820.336960.29118140.29319110.7470.81899.94770.263
2.82-2.9070.37910.26817360.27218290.8050.86999.89060.232
2.907-3.0020.258910.25617230.25618140.8880.8881000.219
3.002-3.1070.333870.24116420.24617290.90.91000.204
3.107-3.2240.271840.22116030.22316880.8920.93199.94080.185
3.224-3.3560.234810.2215310.22116120.9260.9291000.184
3.356-3.5050.323780.22114850.22615630.8820.9161000.191
3.505-3.6750.227750.214260.20215020.930.93899.93340.173
3.675-3.8740.222720.19313510.19414230.9350.951000.175
3.874-4.1080.213670.18912820.1913490.9350.9511000.174
4.108-4.3910.2630.18412100.18512730.9580.9571000.176
4.391-4.7420.195600.17311380.17411980.9620.9621000.167
4.742-5.1930.298540.18910520.19311060.9170.9521000.18
5.193-5.8030.293500.2419470.2439980.9260.94699.89980.227
5.803-6.6960.293460.2268550.239010.9350.9481000.22
6.696-8.1880.21370.1577300.1597670.9660.9731000.165
8.188-11.5270.123310.1095810.116120.9860.9871000.131
11.527-85.620.252200.2183590.223800.9790.9699.73680.246
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)
10.48790.08250.0360.753-1.15982.44420.0242-0.07690.06-0.0278-0.03280.0410.13850.01320.00870.13260.00090.00730.2705-0.01070.01337.402-9.892-20.892
29.20675.0958-3.2145.2783-6.20939.2099-0.31140.27380.6953-0.18410.23610.26420.0408-0.15120.07530.3666-0.00170.03570.39090.03160.29834.582-2.163-30.036
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA144 - 665
2X-RAY DIFFRACTION2ALLPPP628 - 679

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