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- PDB-6wnx: FBXW11-SKP1 in complex with a pSer33/pSer37 Beta-Catenin peptide -

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Basic information

Entry
Database: PDB / ID: 6wnx
TitleFBXW11-SKP1 in complex with a pSer33/pSer37 Beta-Catenin peptide
Components
  • Catenin beta-1
  • F-box/WD repeat-containing protein 11
  • S-phase kinase-associated protein 1
KeywordsLIGASE / Complex / E3 ligase / Structural Genomics / Structural Genomics Consortium / SGC
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 ...: / 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 / microtubule organizing center organization / RUNX3 regulates WNT signaling / regulation of centriole-centriole cohesion / Regulation of CDH11 function / regulation of centromeric sister chromatid cohesion / Specification of the neural plate border / embryonic axis specification / endodermal cell fate commitment / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / F-box domain binding / beta-catenin-TCF complex / lens morphogenesis in camera-type eye / positive regulation of fibroblast growth factor receptor signaling pathway / dorsal root ganglion development / synaptic vesicle clustering / acinar cell differentiation / dorsal/ventral axis specification / proximal/distal pattern formation / neuron fate determination / 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 / PcG protein complex / positive regulation of odontoblast differentiation / vesicle transport along microtubule / cranial skeletal system development / regulation of protein localization to cell surface / hair cell differentiation / cellular response to indole-3-methanol / mesenchymal cell proliferation involved in lung development / endothelial tube morphogenesis / presynaptic active zone cytoplasmic component / detection of muscle stretch / smooth muscle cell differentiation / histone methyltransferase binding / midbrain dopaminergic neuron differentiation / alpha-catenin binding / flotillin complex / establishment of blood-brain barrier / Germ layer formation at gastrulation / negative regulation of oligodendrocyte differentiation / male genitalia development / fascia adherens / apicolateral plasma membrane / epithelial cell proliferation involved in prostate gland development / Formation of definitive endoderm / epithelial cell differentiation involved in prostate gland development / embryonic brain development / positive regulation of epithelial cell proliferation involved in prostate gland development / regulation of smooth muscle cell proliferation / adherens junction assembly / Cul7-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / beta-catenin destruction complex / oocyte development / Formation of axial mesoderm / lung-associated mesenchyme development / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway
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 / F-box-like ...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 / F-box-like / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / 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
Catenin beta-1 / S-phase kinase-associated protein 1 / F-box/WD repeat-containing protein 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsIvanochko, D. / Edwards, A.M. / Bountra, C. / Arrowsmith, C.H. / Boettcher, J. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: FBXW11-SKP1 in complex with a pSer33/pSer37 Beta-Catenin peptide
Authors: Ivanochko, D. / Edwards, A.M. / Bountra, C. / Arrowsmith, C.H. / Boettcher, J.
History
DepositionApr 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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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 11
B: S-phase kinase-associated protein 1
C: Catenin beta-1
D: F-box/WD repeat-containing protein 11
E: S-phase kinase-associated protein 1
F: Catenin beta-1
G: F-box/WD repeat-containing protein 11
H: S-phase kinase-associated protein 1
I: Catenin beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,11517
Polymers200,5169
Non-polymers5998
Water4,990277
1
A: F-box/WD repeat-containing protein 11
B: S-phase kinase-associated protein 1
C: Catenin beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2308
Polymers66,8393
Non-polymers3915
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-48 kcal/mol
Surface area25450 Å2
MethodPISA
2
D: F-box/WD repeat-containing protein 11
E: S-phase kinase-associated protein 1
F: Catenin beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9545
Polymers66,8393
Non-polymers1152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-43 kcal/mol
Surface area25100 Å2
MethodPISA
3
G: F-box/WD repeat-containing protein 11
H: S-phase kinase-associated protein 1
I: Catenin beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9314
Polymers66,8393
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-39 kcal/mol
Surface area25350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.732, 81.866, 133.198
Angle α, β, γ (deg.)90.000, 92.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 6 molecules ADGBEH

#1: Protein F-box/WD repeat-containing protein 11 / F-box and WD repeats protein beta-TrCP2 / F-box/WD repeat-containing protein 1B / Homologous to ...F-box and WD repeats protein beta-TrCP2 / F-box/WD repeat-containing protein 1B / Homologous to Slimb protein / HOS


Mass: 49231.000 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBXW11, BTRCP2, FBW1B, FBXW1B, KIAA0696 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UKB1
#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: 16590.941 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKP1, EMC19, OCP2, SKP1A, TCEB1L / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P63208

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Protein/peptide , 1 types, 3 molecules CFI

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


Mass: 1016.860 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P35222

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Non-polymers , 3 types, 285 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 3.25 Å3/Da / Density % sol: 62.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.12M Ethylene Glycol, 0.1M Morpheus Buffer 1 pH 6.5, 30.0% GOL_P4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00004 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.5→133.02 Å / Num. obs: 78568 / % possible obs: 98.9 % / Redundancy: 6.4 % / CC1/2: 0.984 / Rmerge(I) obs: 0.223 / Rpim(I) all: 0.095 / Rrim(I) all: 0.243 / Net I/σ(I): 5.7
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.478 / Num. unique obs: 4511 / CC1/2: 0.289 / Rpim(I) all: 0.637 / Rrim(I) all: 1.614 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å133.02 Å
Translation2.5 Å133.02 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1p22

1p22


Resolution: 2.5→133.02 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.893 / SU B: 28.108 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.381
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 2632 4.8 %RANDOM
Rwork0.206 ---
obs0.2081 52614 61.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 167.05 Å2 / Biso mean: 60.619 Å2 / Biso min: 7.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å2-0.76 Å2
2---1.05 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 2.5→133.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13320 0 38 277 13635
Biso mean--64.25 33.73 -
Num. residues----1659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01313614
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712750
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.63418429
X-RAY DIFFRACTIONr_angle_other_deg1.2731.58229532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.03451651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.34921.989754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.757152456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.41615109
X-RAY DIFFRACTIONr_chiral_restr0.0650.21792
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215039
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022876
LS refinement shellResolution: 2.501→2.566 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.255 6 -
Rwork0.343 142 -
obs--2.25 %
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)
10.39360.44080.07422.65881.3050.9943-0.07310.1497-0.0387-0.37170.13190.0643-0.1258-0.0642-0.05880.09240.01250.00210.15210.05810.0789-1.667814.151-26.5565
26.31020.50711.6862.14680.43972.15120.047-0.49110.15950.3436-0.1523-0.0322-0.1638-0.25530.10530.12750.03110.0290.16360.06290.0724-18.9233-22.254-36.927
30.32360.86720.02643.9064-0.01140.00640.12220.0402-0.0410.0741-0.10390.1980.02380.0133-0.01820.12690.0349-0.00690.1337-0.05650.14880.736934.5828-11.4428
41.36630.2045-0.09721.39670.1233.47250.0566-0.325-0.01610.29750.0126-0.3055-0.140.5243-0.06920.1665-0.00380.0080.3208-0.04290.138434.906513.1686-58.7925
50.59170.6826-0.67312.57480.9752.4954-0.2830.3520.0867-0.96930.14040.4095-0.2222-0.66880.14250.9897-0.2015-0.20311.7253-0.02810.761150.566645.6932-54.8041
60.79721.6312-1.093.4621-1.37398.65350.03910.00140.12340.07270.02250.28760.36030.022-0.06160.1875-0.01420.00040.18430.01970.171416.33421.0877-69.1228
74.3816-1.0292-1.71390.24390.39640.73580.03450.12380.0536-0.0162-0.03270.00880.08720.0688-0.00180.25740.01530.09120.49270.01270.358755.5122-21.0886-19.9503
82.41182.2404-0.65436.1861-1.15771.6805-0.27710.3734-0.1049-0.56890.2542-0.40680.21270.11840.02280.0623-0.02050.03230.0973-0.01820.030815.0079-24.4784-11.5256
92.5418-1.77950.42654.9581-6.20239.46250.1526-0.2634-0.3729-0.49260.09260.35790.62340.05-0.24520.1729-0.0092-0.06390.3927-0.00180.16974.9835-26.9861-34.5921
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 701
2X-RAY DIFFRACTION2B2 - 201
3X-RAY DIFFRACTION3C31 - 39
4X-RAY DIFFRACTION4D2 - 601
5X-RAY DIFFRACTION5E4 - 139
6X-RAY DIFFRACTION6F31 - 39
7X-RAY DIFFRACTION7G1 - 501
8X-RAY DIFFRACTION8H2 - 145
9X-RAY DIFFRACTION9I31 - 39

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