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- PDB-6m90: Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-277... -

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Open data


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Basic information

Entry
Database: PDB / ID: 6m90
TitleMonophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2776 ternary complex
Components
  • Catenin beta-1
  • F-box/WD repeat-containing protein 1A
  • Skp1
KeywordsLIGASE / Ubiquitin Molecular Glue Enhancer
Function / homology
Function and homology information


protein phosphorylated amino acid binding / 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 / beta-catenin-ICAT complex ...protein phosphorylated amino acid binding / 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 / beta-catenin-ICAT complex / CDH11 homotypic and heterotypic interactions / genitalia morphogenesis / embryonic skeletal limb joint morphogenesis / canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / neural plate development / metanephros morphogenesis / glial cell fate determination / Regulation of CDH19 Expression and Function / regulation of secondary heart field cardioblast proliferation / astrocyte-dopaminergic neuron signaling / oviduct development / beta-catenin-TCF7L2 complex / regulation of nephron tubule epithelial cell differentiation / regulation of timing of anagen / negative regulation of mitotic cell cycle, embryonic / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / Binding of TCF/LEF:CTNNB1 to target gene promoters / central nervous system vasculogenesis / regulation of centriole-centriole cohesion / RUNX3 regulates WNT signaling / regulation of centromeric sister chromatid cohesion / Regulation of CDH11 function / embryonic axis specification / Specification of the neural plate border / lens morphogenesis in camera-type eye / Scrib-APC-beta-catenin complex / regulation of fibroblast proliferation / beta-catenin-TCF complex / acinar cell differentiation / synaptic vesicle clustering / dorsal root ganglion development / endodermal cell fate commitment / neuron fate determination / proximal/distal pattern formation / F-box domain binding / Formation of the nephric duct / endothelial tube morphogenesis / positive regulation of fibroblast growth factor receptor signaling pathway / sympathetic ganglion development / dorsal/ventral axis specification / layer formation in cerebral cortex / presynaptic active zone cytoplasmic component / positive regulation of endothelial cell differentiation / fungiform papilla formation / mesenchymal to epithelial transition / hindbrain development / positive regulation of skeletal muscle tissue development / positive regulation of determination of dorsal identity / fascia adherens / lung epithelial cell differentiation / regulation of protein localization to cell surface / hair cell differentiation / ectoderm development / embryonic foregut morphogenesis / cellular response to indole-3-methanol / detection of muscle stretch / positive regulation of odontoblast differentiation / smooth muscle cell differentiation / mesenchymal cell proliferation involved in lung development / positive regulation of myoblast proliferation / PcG protein complex / alpha-catenin binding / histone methyltransferase binding / regulation of epithelial to mesenchymal transition / Germ layer formation at gastrulation / regulation of calcium ion import / positive regulation of homotypic cell-cell adhesion / negative regulation of oligodendrocyte differentiation / establishment of blood-retinal barrier / apicolateral plasma membrane / flotillin complex / epithelial cell differentiation involved in prostate gland development / positive regulation of epithelial cell proliferation involved in prostate gland development / cranial skeletal system development / cell-cell adhesion mediated by cadherin / male genitalia development / Formation of definitive endoderm / epithelial cell proliferation involved in prostate gland development / catenin complex / embryonic brain development / positive regulation of circadian rhythm / positive regulation of ubiquitin protein ligase activity / lung-associated mesenchyme development / oocyte development / regulation of smooth muscle cell proliferation / establishment of blood-brain barrier / midbrain dopaminergic neuron differentiation / Formation of axial mesoderm / beta-catenin destruction complex / Cul7-RING ubiquitin ligase complex
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 / F-box-like domain superfamily ...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 / 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 domain / Monooxygenase / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / 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 / SKP1/BTB/POZ domain superfamily / 7 Propeller / Methylamine Dehydrogenase; Chain H / Armadillo-like helical / WD domain, G-beta repeat / 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. / 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-J91 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSimonetta, K.R. / Clifton, M.C. / Walter, R.L. / Ranieri, G.M. / Carter, J.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 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Skp1
C: Catenin beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3906
Polymers69,4233
Non-polymers9683
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-41 kcal/mol
Surface area24000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.760, 82.760, 111.820
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 Skp1


Mass: 16459.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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, 77 molecules

#4: Chemical ChemComp-J91 / 2-(2-fluorophenoxy)-3-{[2-oxo-6-(trifluoromethyl)-1,2-dihydropyridine-3-carbonyl]amino}benzoic acid


Mass: 436.313 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H12F4N2O5 / 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.: 74 / 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: 3.3 Å3/Da / Density % sol: 62.77 %
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: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→27.695 Å / Num. obs: 53275 / % possible obs: 99.2 % / Redundancy: 4.849 % / Biso Wilson estimate: 51.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.048 / Χ2: 0.991 / Net I/σ(I): 18.33 / Num. measured all: 258335 / Scaling rejects: 17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.05-2.14.8011.4341.0918848397239260.331.60898.8
2.1-2.164.8711.0821.518569384538120.4821.21399.1
2.16-2.224.8850.8421.9518329378137520.6660.94399.2
2.22-2.294.8850.6322.6517787366936410.7720.70899.2
2.29-2.374.8890.4633.5717345356535480.8590.51899.5
2.37-2.454.9020.3434.7116572340433810.9160.38499.3
2.45-2.544.8890.2636.1316013329232750.9490.29499.5
2.54-2.654.9060.1769.0515738321632080.9750.19899.8
2.65-2.764.8960.11912.7914946306630530.9880.13399.6
2.76-2.94.9110.08616.9814326292429170.9940.09699.8
2.9-3.064.8940.06322.2513512276627610.9970.07199.8
3.06-3.244.8810.04629.4312823263126270.9980.05299.8
3.24-3.474.8370.03537.5511952247224710.9990.039100
3.47-3.744.7940.02944.2410897227622730.9990.03399.9
3.74-4.14.7650.02648.2310160213521320.9990.02999.9
4.1-4.584.7630.02452.728998189018890.9990.02799.9
4.58-5.294.7490.02354.458031169116910.9990.026100
5.29-6.484.7960.02253.386854143114290.9990.02499.9
6.48-9.174.6660.02155.255044110110810.9990.02498.2
9.17-27.6953.90.02250.7915915934080.9980.02668.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P22

1p22


Resolution: 2.05→27.695 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 22.32
RfactorNum. reflection% reflection
Rfree0.2116 2010 3.77 %
Rwork0.1784 --
obs0.1796 53265 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.88 Å2 / Biso mean: 66.8582 Å2 / Biso min: 38.71 Å2
Refinement stepCycle: final / Resolution: 2.05→27.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4266 0 67 74 4407
Biso mean--62.49 55.77 -
Num. residues----547
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 (%)
2.0501-2.10140.34181410.29863620376199
2.1014-2.15820.2941500.27033648379899
2.1582-2.22170.28361400.2493649378999
2.2217-2.29340.28331460.22843692383899
2.2934-2.37530.23461460.21223660380699
2.3753-2.47030.25731460.208936753821100
2.4703-2.58270.25361540.199536823836100
2.5827-2.71870.24151440.200236593803100
2.7187-2.88890.25281460.198436963842100
2.8889-3.11170.23111420.20536813823100
3.1117-3.42430.24461420.193336933835100
3.4243-3.91860.20171320.171337013833100
3.9186-4.93250.16561440.137937013845100
4.9325-27.69710.18511370.16293498363595
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)
10.28560.19440.15560.4819-0.40930.670.30940.32960.6804-0.3632-0.2075-0.56150.0928-0.04060.00310.760.23540.05070.47560.05890.8498-21.383369.46068.0972
20.1036-0.1938-0.05270.18650.12510.1901-0.06250.3859-0.7271-0.33460.4042-0.0990.4040.1270.01180.6680.17740.04880.7091-0.00090.57982.3355.8318-6.7921
31.2120.733-0.68250.7508-0.28650.40750.26590.1111-0.3326-0.1117-0.20520.12520.28470.151700.88080.261-0.05560.5219-0.0920.5114-36.950456.9668.5273
41.87040.27290.08441.11910.2002-0.0658-0.0170.32490.02850.0864-0.184-0.49680.0166-0.1938-0.00010.76880.26360.06610.4959-0.08080.6072-23.30554.43749.8502
50.1173-0.08280.47420.1432-0.61783.2976-0.75870.0658-1.36340.2005-0.28710.4815-0.0288-0.0452-0.10790.91940.33890.00120.5525-0.05651.1011-10.163939.307810.2934
60.0509-0.05570.01880.0633-0.02460.0158-0.328-1.2017-0.08070.48540.3832-0.71970.8540.6341-0.00431.0260.3965-0.05510.77450.10350.8553-13.907643.644318.9031
71.24810.17910.54530.2957-0.02280.42960.05980.0380.6177-0.06610.0582-1.0145-0.3453-0.0373-0.07820.75310.2145-0.04260.49280.00270.9998-8.009548.05057.4979
80.95650.9131-0.30971.6854-0.93570.7753-0.1456-0.20940.44230.86140.2066-0.4954-0.04240.1871-0.01430.62910.2167-0.09180.5568-0.09050.61054.164518.853110.5282
91.1305-0.1139-0.62230.5872-0.31930.6076-0.0044-0.27280.11970.60560.13820.00360.0233-0.27370.10150.67580.2501-0.0360.5183-0.0640.4675-0.228514.350613.7431
100.91790.4592-0.05260.5823-0.62890.76290.2585-0.13940.40930.4085-0.1407-0.0744-0.2274-0.3692-0.00150.78250.2270.09630.6332-0.00080.4955-8.08678.142511.5305
112.35450.4655-0.12091.2025-0.5190.2621-0.01780.02870.02110.43010.16550.2237-0.0729-0.214-0.00010.65860.18770.04370.52510.02760.4516-9.68896.25848.5835
121.01430.8627-0.03771.1324-0.62420.66870.124-0.0994-0.2403-0.17170.07110.57980.0854-0.53640.00070.65560.12840.05680.66830.08660.5964-14.49855.50430.6701
131.596-0.2470.46781.5474-0.4441.1035-0.00870.21990.0043-0.03410.10760.45550.1727-0.49050.00010.51270.13980.00890.6110.0780.5461-15.69898.5876-4.5906
140.41430.06570.8281.4763-0.06861.52730.08190.32330.3477-0.0213-0.01440.1553-0.0821-0.34520.00010.49370.18140.00860.64470.05350.5502-13.972514.0415-11.0169
151.2060.97780.2662.45510.48852.4763-0.09650.39110.5712-0.32470.07820.0214-0.4926-0.03210.17060.54590.1780.04750.53830.13660.6561-4.452926.3126-10.8355
160.73370.71650.82231.23030.06641.4858-0.1029-0.13780.4560.32080.0293-0.2861-0.17380.374900.57710.17090.00710.4841-0.03760.73863.212825.79683.775
172.66190.488-1.25710.4703-0.03680.7133-0.11120.624-0.5979-0.4191-0.0750.50980.9327-0.5743-0.01191.201-0.1355-0.18760.6053-0.27780.7521-55.821942.73927.4935
180.2020.10020.04370.2199-0.13630.1625-0.35690.549-0.5125-0.3715-0.1938-0.28270.39650.5561-0.00671.54230.04270.03980.8977-0.38881.0789-39.429739.4907-2.6786
191.56951.57530.31331.31570.24310.75370.05270.5878-0.327-0.3723-0.09330.18170.5431-0.1590.01281.06030.1552-0.09930.5644-0.17340.5221-41.685349.90451.5561
203.592-0.3781.01330.7322-0.08650.2834-0.37721.01071.1427-0.86740.2363-0.6517-0.62850.12-0.17270.94570.25970.15430.6404-0.05440.4859-28.27363.6255-2.0495
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 122 through 139 )B122 - 139
2X-RAY DIFFRACTION2chain 'C' and (resid 31 through 40 )C31 - 40
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 163 )A138 - 163
4X-RAY DIFFRACTION4chain 'A' and (resid 164 through 199 )A164 - 199
5X-RAY DIFFRACTION5chain 'A' and (resid 200 through 210 )A200 - 210
6X-RAY DIFFRACTION6chain 'A' and (resid 211 through 217 )A211 - 217
7X-RAY DIFFRACTION7chain 'A' and (resid 227 through 252 )A227 - 252
8X-RAY DIFFRACTION8chain 'A' and (resid 253 through 293 )A253 - 293
9X-RAY DIFFRACTION9chain 'A' and (resid 294 through 315 )A294 - 315
10X-RAY DIFFRACTION10chain 'A' and (resid 316 through 333 )A316 - 333
11X-RAY DIFFRACTION11chain 'A' and (resid 334 through 356 )A334 - 356
12X-RAY DIFFRACTION12chain 'A' and (resid 357 through 374 )A357 - 374
13X-RAY DIFFRACTION13chain 'A' and (resid 375 through 416 )A375 - 416
14X-RAY DIFFRACTION14chain 'A' and (resid 417 through 439 )A417 - 439
15X-RAY DIFFRACTION15chain 'A' and (resid 440 through 516 )A440 - 516
16X-RAY DIFFRACTION16chain 'A' and (resid 517 through 548 )A517 - 548
17X-RAY DIFFRACTION17chain 'B' and (resid 2 through 58 )B2 - 58
18X-RAY DIFFRACTION18chain 'B' and (resid 59 through 68 )B59 - 68
19X-RAY DIFFRACTION19chain 'B' and (resid 69 through 109 )B69 - 109
20X-RAY DIFFRACTION20chain 'B' and (resid 110 through 121 )B110 - 121

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