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- PDB-1p22: Structure of a beta-TrCP1-Skp1-beta-catenin complex: destruction ... -

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Basic information

Entry
Database: PDB / ID: 1p22
TitleStructure of a beta-TrCP1-Skp1-beta-catenin complex: destruction motif binding and lysine specificity on the SCFbeta-TrCP1 ubiquitin ligase
Components
  • Beta-catenin
  • F-box/WD-repeat protein 1A
  • Skp1
KeywordsSIGNALING PROTEIN / Ubiquitination / degradation
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 / Binding of TCF/LEF:CTNNB1 to target gene promoters / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / 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 / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / lens morphogenesis in camera-type eye / beta-catenin-TCF complex / endodermal cell fate commitment / acinar cell differentiation / dorsal root ganglion development / synaptic vesicle clustering / positive regulation of fibroblast growth factor receptor signaling pathway / proximal/distal pattern formation / neuron fate determination / F-box domain binding / Formation of the nephric duct / endothelial tube morphogenesis / layer formation in cerebral cortex / dorsal/ventral axis specification / sympathetic ganglion development / establishment of blood-retinal barrier / positive regulation of myoblast proliferation / fungiform papilla formation / positive regulation of endothelial cell differentiation / presynaptic active zone cytoplasmic component / mesenchymal to epithelial transition / hindbrain development / lung epithelial cell differentiation / positive regulation of determination of dorsal identity / positive regulation of skeletal muscle tissue development / ectoderm development / fascia adherens / regulation of protein localization to cell surface / embryonic foregut morphogenesis / hair cell differentiation / detection of muscle stretch / cellular response to indole-3-methanol / smooth muscle cell differentiation / positive regulation of odontoblast differentiation / mesenchymal cell proliferation involved in lung development / histone methyltransferase binding / PcG protein complex / alpha-catenin binding / regulation of calcium ion import / Germ layer formation at gastrulation / regulation of epithelial to mesenchymal transition / positive regulation of homotypic cell-cell adhesion / establishment of blood-brain barrier / negative regulation of oligodendrocyte differentiation / flotillin complex / apicolateral plasma membrane / epithelial cell differentiation involved in prostate gland development / cranial skeletal system development / positive regulation of epithelial cell proliferation involved in prostate gland development / cell-cell adhesion mediated by cadherin / male genitalia development / Formation of definitive endoderm / regulation of smooth muscle cell proliferation / epithelial cell proliferation involved in prostate gland development / catenin complex / positive regulation of ubiquitin protein ligase activity / beta-catenin destruction complex / embryonic brain development / ubiquitin ligase activator activity / positive regulation of circadian rhythm / oocyte development / lung-associated mesenchyme development / midbrain dopaminergic neuron differentiation / 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 / SKP1/BTB/POZ domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 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
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 / MAD / Resolution: 2.95 Å
AuthorsWu, G. / Xu, G. / Schulman, B.A. / Jeffrey, P.D. / Harper, J.W. / Pavletich, N.P.
CitationJournal: Mol.Cell / Year: 2003
Title: Structure of a beta-TrCP1-Skp1-beta-Catenin complex: destruction motif binding and lysine specificity of the SCFbeta-TrCP1 ubiquitin ligase
Authors: Wu, G. / Xu, G. / Schulman, B.A. / Jeffrey, P.D. / Harper, J.W. / Pavletich, N.P.
History
DepositionApr 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 999an appropriate sequence database reference for Skp1, chain B, was not available at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F-box/WD-repeat protein 1A
B: Skp1
C: Beta-catenin


Theoretical massNumber of molelcules
Total (without water)69,1963
Polymers69,1963
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-39 kcal/mol
Surface area24770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.6, 82.6, 111.5
Angle α, β, γ (deg.)90, 90, 120
Int Tables number144
Space group name H-MP31

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Components

#1: Protein F-box/WD-repeat protein 1A / F-box and WD-repeats protein beta-TrCP / E3RSIkappaB / pIkappaBalpha-E3 receptor subunit


Mass: 49699.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y297
#2: Protein Skp1


Mass: 16590.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63208
#3: Protein/peptide Beta-catenin / PRO2286


Mass: 2904.903 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTNNB1 OR CTNNB / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35222
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: 3.17 Å3/Da / Density % sol: 61.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG4000, sodium citrate, Bis-Tris Propane, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
25 mg/mlbeta-catenin peptide1drop
316-20 %PEG40001reservoir
4320 mMsodium citrate1reservoir
5100 mMBTP1reservoirpH6.8

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 23, 2001
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.95→20 Å / Num. all: 17628 / Num. obs: 17628 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rsym value: 0.04
Reflection shellResolution: 2.95→3.025 Å / % possible all: 99.3
Reflection
*PLUS
Num. measured all: 52111 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
Highest resolution: 2.95 Å / Rmerge(I) obs: 0.43

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
DMmodel building
REFMAC5.1refinement
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.95→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28554 840 -RANDOM
Rwork0.2304 ---
all0.23315 16793 --
obs0.23315 16793 99.3 %-
Refinement stepCycle: LAST / Resolution: 2.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4340 0 0 0 4340
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.014
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.855
LS refinement shell
*PLUS
Highest resolution: 2.95 Å / Lowest resolution: 3.025 Å / Rfactor Rfree: 0.511 / Rfactor Rwork: 0.433 / Num. reflection Rwork: 1201

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