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- PDB-6m93: Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-193... -

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Basic information

Entry
Database: PDB / ID: 6m93
TitleMonophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-1933 ternary complex
Components
  • Catenin beta-1
  • F-box/WD repeat-containing protein 1A
  • S-phase kinase-associated protein 1
KeywordsLIGASE / Ubiquitin Molecular Glue Enhancer
Function / homology
Function and homology information


protein phosphorylated amino acid 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 ...protein phosphorylated amino acid 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 / 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 / F-box domain binding / 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 / PcG protein complex / 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 / positive regulation of ubiquitin protein ligase activity / ubiquitin ligase activator activity / Cul7-RING ubiquitin ligase complex / embryonic brain development / beta-catenin destruction complex / adherens junction assembly / positive regulation of circadian rhythm / oocyte development / maintenance of protein location in nucleus / Formation of axial mesoderm / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling
Similarity search - Function
D domain of beta-TrCP / D domain of beta-TrCP / D domain of beta-TrCP / : / Monooxygenase - #50 / Beta-catenin / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / SKP1 component, dimerisation ...D domain of beta-TrCP / D domain of beta-TrCP / D domain of beta-TrCP / : / Monooxygenase - #50 / Beta-catenin / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box-like / F-box domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Monooxygenase / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Armadillo/beta-catenin-like repeats / Armadillo / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / SKP1/BTB/POZ domain superfamily / Armadillo-like helical / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-J8Y / PHOSPHATE ION / Catenin beta-1 / S-phase kinase-associated protein 1 / F-box/WD repeat-containing protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsSimonetta, K.R. / Clifton, M.C. / Walter, R.L. / Ranieri, G.M. / Lee, S.J.
CitationJournal: Nat Commun / Year: 2019
Title: Prospective discovery of small molecule enhancers of an E3 ligase-substrate interaction.
Authors: Simonetta, K.R. / Taygerly, J. / Boyle, K. / Basham, S.E. / Padovani, C. / Lou, Y. / Cummins, T.J. / Yung, S.L. / von Soly, S.K. / Kayser, F. / Kuriyan, J. / Rape, M. / Cardozo, M. / Gallop, ...Authors: Simonetta, K.R. / Taygerly, J. / Boyle, K. / Basham, S.E. / Padovani, C. / Lou, Y. / Cummins, T.J. / Yung, S.L. / von Soly, S.K. / Kayser, F. / Kuriyan, J. / Rape, M. / Cardozo, M. / Gallop, M.A. / Bence, N.F. / Barsanti, P.A. / Saha, A.
History
DepositionAug 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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
A: F-box/WD repeat-containing protein 1A
B: S-phase kinase-associated protein 1
C: Catenin beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8685
Polymers69,4233
Non-polymers4452
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-40 kcal/mol
Surface area23160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.530, 82.530, 111.260
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein F-box/WD repeat-containing protein 1A / E3RSIkappaB / Epididymis tissue protein Li 2a / F-box and WD repeats protein beta-TrCP / ...E3RSIkappaB / Epididymis tissue protein Li 2a / F-box and WD repeats protein beta-TrCP / pIkappaBalpha-E3 receptor subunit


Mass: 49418.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTRC, BTRCP, FBW1A, FBXW1A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y297
#2: Protein S-phase kinase-associated protein 1 / Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti ...Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti protein II / OCP-II / RNA polymerase II elongation factor-like protein / SIII / Transcription elongation factor B polypeptide 1-like / p19skp1


Mass: 16459.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKP1, EMC19, OCP2, SKP1A, TCEB1L / Production host: Escherichia coli (E. coli) / References: UniProt: P63208

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Protein/peptide , 1 types, 1 molecules C

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


Mass: 3544.714 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P35222

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Non-polymers , 3 types, 16 molecules

#4: Chemical ChemComp-J8Y / 2-oxo-N-[3-(1H-tetrazol-5-yl)phenyl]-6-(trifluoromethyl)-1,2-dihydropyridine-3-carboxamide


Mass: 350.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H9F3N6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.15 Å3/Da / Density % sol: 60.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 8% PEG 4000 0.1M BTP pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→41.265 Å / Num. obs: 29168 / % possible obs: 99.5 % / Redundancy: 4.115 % / Biso Wilson estimate: 73.77 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.134 / Χ2: 0.957 / Net I/σ(I): 10.91
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.574.4361.940.9421730.3192.201100
2.57-2.644.4391.41.2820890.4241.589100
2.64-2.714.411.041.7720500.6091.183100
2.71-2.84.3820.7332.5520000.7570.834100
2.8-2.894.320.5433.3719540.8860.62100
2.89-2.994.2640.4074.4618580.9150.465100
2.99-3.14.2290.3096.1417940.9410.35499.9
3.1-3.234.1240.2158.4817580.9720.24799.9
3.23-3.374.0860.1711.4116620.9850.19699.8
3.37-3.543.9790.12514.2415850.9880.14499.9
3.54-3.733.9280.10217.1215190.990.11899.9
3.73-3.953.8660.09218.914590.9930.10799.5
3.95-4.233.8330.07820.9413050.9930.09199.5
4.23-4.563.7560.07122.5612390.9930.08398.9
4.56-53.7680.06424.0211390.9960.07499.5
5-5.593.7520.07623.4910330.9920.08998.8
5.59-6.463.8780.11523.579260.9820.13399
6.46-7.913.8630.14124.77670.9810.16399.4
7.91-11.183.6480.08725.545710.980.10396.1
11.18-41.2653.30.09323.082870.9740.11186.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 2.5→41.265 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 27.07
RfactorNum. reflection% reflection
Rfree0.23 2013 6.91 %
Rwork0.2135 --
obs0.2147 29129 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 154.71 Å2 / Biso mean: 90.1758 Å2 / Biso min: 52.49 Å2
Refinement stepCycle: final / Resolution: 2.5→41.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4123 0 30 14 4167
Biso mean--77.61 69.52 -
Num. residues----542
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5001-2.56260.34641400.315819392079100
2.5626-2.63190.31151380.290419342072100
2.6319-2.70930.33531540.291919662120100
2.7093-2.79680.30841420.285919142056100
2.7968-2.89670.32631440.280119662110100
2.8967-3.01260.31151420.26819542096100
3.0126-3.14970.28351480.258719552103100
3.1497-3.31570.28431540.251219572111100
3.3157-3.52330.25881350.230119282063100
3.5233-3.79520.23681440.213819372081100
3.7952-4.17680.22191490.20111949209899
4.1768-4.78040.16891330.16531950208399
4.7804-6.01980.20451520.19141915206799
6.0198-41.27060.1971380.19951852199095
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)
10.0323-0.0233-0.01360.03140.04530.04210.0724-0.13690.024-0.05840.09980.11710.36950.08890.00021.3722-0.38380.53261.62590.03811.11385.9045-73.7519-9.3383
20.04450.0156-0.00740.0198-0.01010.00250.2445-0.2798-0.20670.68-0.2632-0.415-0.0899-0.293501.10430.02860.30421.60380.10480.81459.1319-75.7508-6.3631
30.04670.0245-0.00380.0142-0.00960.01530.10720.07110.0183-0.1352-0.38010.3026-0.14310.09560.00021.15870.46590.1661.7964-0.29511.24375.1545-62.3158-8.3512
40.0147-0.0042-0.00770.028-0.01480.0388-0.34820.05470.0429-0.18610.4170.5253-0.0127-0.198400.80860.30010.26591.68050.17681.26896.6697-64.7422-16.5233
50.0320.03520.05670.05050.06880.1086-0.8626-0.38270.1820.0342-0.29170.2314-0.2306-0.2635-0.00641.10320.16540.28862.37190.11621.26443.285-70.9967-18.9775
60.0737-0.13190.06760.2174-0.12270.0688-0.42530.191-0.10730.5238-0.4234-0.6325-0.221-0.46920.00020.95420.06880.38281.33950.06550.95314.5934-73.1369-12.4196
71.0621-0.48170.57070.4457-0.16940.3138-0.249-1.00920.62810.4006-0.5381-0.2242-0.5779-0.5956-0.07661.30170.12160.60951.43830.140.973612.9095-66.1704-0.9685
80.24590.8422-0.36443.3032-1.50720.7081-0.4499-0.6602-0.23940.5987-1.4013-0.1395-0.2668-0.2625-0.30581.39420.16340.27771.6664-0.18190.822818.6302-59.66524.9669
90.16410.1902-0.01340.1771-0.02930.02970.31150.0111-0.55661.3742-0.1470.63550.4986-0.39160.00061.16240.32380.23071.21310.06870.848721.4563-64.5247-7.9146
101.3291-0.98511.03550.7677-0.82580.9382-0.30710.07870.28960.9273-0.17510.4426-0.5525-0.2169-0.13221.30590.48430.27381.1411-0.10480.795524.0109-55.3601-3.4367
111.69291.2296-0.09131.7777-0.19240.02790.1676-1.0641-0.45831.0566-0.4007-0.5570.26770.5007-0.07751.41010.4612-0.07920.7917-0.19010.749442.6849-57.4814-2.6423
120.0510.0195-0.04150.008-0.01390.0228-0.67430.1917-0.01120.03920.47990.31160.1156-0.409900.98060.2432-0.16451.05410.27681.573150.8056-48.7889-10.1095
130.02390.0179-0.00550.03740.06150.0490.4903-0.28480.43480.4458-0.0988-0.12910.3256-0.077400.87490.06190.06570.5826-0.07750.71576.0739-0.63245.747
141.0197-0.26830.30160.85090.52850.28920.0115-0.07430.4641-0.0711-0.0811-0.25770.20090.11010.01181.00580.33370.07010.6642-0.06330.917133.687-43.649-11.4505
152.8972-0.2947-0.33781.9711-0.31272.48740.16460.0856-0.1186-0.00040.0106-0.28340.161-0.1397-00.76880.137-0.07010.4175-0.03150.647511.4286-13.167-1.5616
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 3 through 8 )B3 - 8
2X-RAY DIFFRACTION2chain 'B' and (resid 9 through 17 )B9 - 17
3X-RAY DIFFRACTION3chain 'B' and (resid 18 through 24 )B18 - 24
4X-RAY DIFFRACTION4chain 'B' and (resid 25 through 32 )B25 - 32
5X-RAY DIFFRACTION5chain 'B' and (resid 33 through 38 )B33 - 38
6X-RAY DIFFRACTION6chain 'B' and (resid 39 through 45 )B39 - 45
7X-RAY DIFFRACTION7chain 'B' and (resid 46 through 58 )B46 - 58
8X-RAY DIFFRACTION8chain 'B' and (resid 59 through 78 )B59 - 78
9X-RAY DIFFRACTION9chain 'B' and (resid 79 through 94 )B79 - 94
10X-RAY DIFFRACTION10chain 'B' and (resid 95 through 109 )B95 - 109
11X-RAY DIFFRACTION11chain 'B' and (resid 110 through 128 )B110 - 128
12X-RAY DIFFRACTION12chain 'B' and (resid 129 through 139 )B129 - 139
13X-RAY DIFFRACTION13chain 'C' and (resid 30 through 40 )C30 - 40
14X-RAY DIFFRACTION14chain 'A' and (resid 138 through 252 )A138 - 252
15X-RAY DIFFRACTION15chain 'A' and (resid 253 through 547 )A253 - 547

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