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- PDB-4o1v: SPOP Promotes Tumorigenesis by Acting as a Key Regulatory Hub in ... -

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Basic information

Entry
Database: PDB / ID: 4o1v
TitleSPOP Promotes Tumorigenesis by Acting as a Key Regulatory Hub in Kidney Cancer
Components
  • Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
  • Speckle-type POZ protein
KeywordsPROTEIN BINDING / UBL conjugation pathway / ligase / ubiquitin / E3 / SPOP / MATH / PTEN
Function / homology
Function and homology information


PTEN Loss of Function in Cancer / inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / phosphatidylinositol phosphate phosphatase activity / rhythmic synaptic transmission / inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity / central nervous system myelin maintenance ...PTEN Loss of Function in Cancer / inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / phosphatidylinositol phosphate phosphatase activity / rhythmic synaptic transmission / inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity / central nervous system myelin maintenance / negative regulation of wound healing, spreading of epidermal cells / phosphatidylinositol-3-phosphate phosphatase activity / central nervous system neuron axonogenesis / postsynaptic density assembly / neuron-neuron synaptic transmission / presynaptic membrane assembly / Regulation of PTEN mRNA translation / synapse maturation / Negative regulation of the PI3K/AKT network / negative regulation of cell cycle G1/S phase transition / cellular response to electrical stimulus / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of axonogenesis / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / Transcriptional Regulation by MECP2 / myelin sheath adaxonal region / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of organ growth / negative regulation of excitatory postsynaptic potential / forebrain morphogenesis / negative regulation of focal adhesion assembly / phosphatidylinositol dephosphorylation / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / anaphase-promoting complex binding / Schmidt-Lanterman incisure / dentate gyrus development / ubiquitin ligase activator activity / positive regulation of ubiquitin protein ligase activity / phosphatidylinositol biosynthetic process / dendritic spine morphogenesis / negative regulation of cell size / maternal behavior / spindle assembly involved in female meiosis / negative regulation of peptidyl-serine phosphorylation / positive regulation of ubiquitin-dependent protein catabolic process / negative regulation of epithelial to mesenchymal transition / molecular function inhibitor activity / Cul3-RING ubiquitin ligase complex / protein serine/threonine phosphatase activity / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / negative regulation of G1/S transition of mitotic cell cycle / regulation of neuron projection development / ubiquitin-specific protease binding / Synthesis of IP3 and IP4 in the cytosol / social behavior / locomotor rhythm / adult behavior / negative regulation of vascular associated smooth muscle cell proliferation / Synthesis of PIPs at the plasma membrane / positive regulation of intracellular signal transduction / phosphoprotein phosphatase activity / regulation of proteolysis / negative regulation of cellular senescence / positive regulation of excitatory postsynaptic potential / negative regulation of osteoblast differentiation / prepulse inhibition / multicellular organismal response to stress / synapse assembly / protein dephosphorylation / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Regulation of PTEN localization / negative regulation of cell migration / central nervous system development / cell projection / PDZ domain binding / TP53 Regulates Metabolic Genes / locomotory behavior / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell motility / Hedgehog 'on' state / regulation of protein stability / beta-catenin binding / PML body / cytoplasmic side of plasma membrane / Regulation of PTEN stability and activity / protein polyubiquitination
Similarity search - Function
Bifunctional phosphatidylinositol trisphosphate phosphatase/dual specificity phosphatase PTEN / PTEN, phosphatase domain / : / Inositol hexakisphosphate / SPOP, C-terminal BACK domain / : / BPM/SPOP, BACK domain / MATH domain / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain ...Bifunctional phosphatidylinositol trisphosphate phosphatase/dual specificity phosphatase PTEN / PTEN, phosphatase domain / : / Inositol hexakisphosphate / SPOP, C-terminal BACK domain / : / BPM/SPOP, BACK domain / MATH domain / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / Polymorphic toxin system, DSP-PTPase phosphatase / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / C2 domain superfamily / SKP1/BTB/POZ domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Speckle-type POZ protein / Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCalabrese, M.F. / Watson, E.R. / Schulman, B.A.
CitationJournal: Cancer Cell / Year: 2014
Title: SPOP Promotes Tumorigenesis by Acting as a Key Regulatory Hub in Kidney Cancer.
Authors: Li, G. / Ci, W. / Karmakar, S. / Chen, K. / Dhar, R. / Fan, Z. / Guo, Z. / Zhang, J. / Ke, Y. / Wang, L. / Zhuang, M. / Hu, S. / Li, X. / Zhou, L. / Li, X. / Calabrese, M.F. / Watson, E.R. / ...Authors: Li, G. / Ci, W. / Karmakar, S. / Chen, K. / Dhar, R. / Fan, Z. / Guo, Z. / Zhang, J. / Ke, Y. / Wang, L. / Zhuang, M. / Hu, S. / Li, X. / Zhou, L. / Li, X. / Calabrese, M.F. / Watson, E.R. / Prasad, S.M. / Rinker-Schaeffer, C. / Eggener, S.E. / Stricker, T. / Tian, Y. / Schulman, B.A. / Liu, J. / White, K.P.
History
DepositionDec 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Speckle-type POZ protein
B: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN


Theoretical massNumber of molelcules
Total (without water)18,0192
Polymers18,0192
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-4 kcal/mol
Surface area7490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.500, 56.158, 42.611
Angle α, β, γ (deg.)90.00, 97.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Speckle-type POZ protein / HIB homolog 1 / Roadkill homolog 1


Mass: 16543.967 Da / Num. of mol.: 1 / Fragment: MATH domain (UNP residues 28-166)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPOP / Production host: Escherichia coli (E. coli) / References: UniProt: O43791
#2: Protein/peptide Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN / Mutated in multiple advanced cancers 1 / Phosphatase and tensin homolog


Mass: 1475.469 Da / Num. of mol.: 1 / Fragment: UNP residues 354-368 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P60484
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

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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: 1.99 Å3/Da / Density % sol: 38.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris, 100 mM sodium malonate, 36% PEG400, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2011
RadiationMonochromator: double crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 9584 / % possible obs: 99.9 % / Redundancy: 3.7 %
Reflection shellHighest resolution: 2 Å

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IVV

3ivv


Resolution: 2→40.99 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 11.216 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 495 5.2 %RANDOM
Rwork0.192 ---
obs0.193 9085 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0 Å20.1 Å2
2---0.35 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 2→40.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1155 0 0 105 1260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221178
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0161.961583
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0065146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64623.87849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20415210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.877156
X-RAY DIFFRACTIONr_chiral_restr0.0710.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02865
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3221.5734
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.60721169
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0993444
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8194.5414
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 31 -
Rwork0.246 621 -
obs--92.35 %
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)
13.86121.01932.09814.28371.67955.98110.1863-0.1614-0.4110.427-0.0883-0.30780.48810.269-0.0980.0792-0.0004-0.00610.09910.04420.14489.8492.6446.94
224.2768-4.6307-4.85144.54040.523940.34280.42031.3276-0.0349-0.8563-0.6671-1.8058-0.30851.53930.24690.1321-0.13790.10480.4041-0.170.431623.0929.339-1.989
39.22765.83088.00578.08916.57499.1196-0.02980.2594-0.81880.28840.5413-1.35820.20330.8084-0.51140.06420.0445-0.04910.2022-0.00370.317821.3176.5066.951
43.12212.6381.38937.06143.28025.0367-0.13420.12230.0133-0.24680.2137-0.2306-0.44550.2499-0.07950.0338-0.021-0.01020.09490.0340.075614.90210.7262.893
54.69952.42516.65726.01034.901329.2392-0.0417-0.10990.01920.07040.03150.1696-0.8562-0.10780.01030.0327-0.0317-0.01630.05240.03640.07538.99910.6598.432
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 64
2X-RAY DIFFRACTION2B357 - 363
3X-RAY DIFFRACTION3A65 - 84
4X-RAY DIFFRACTION4A85 - 147
5X-RAY DIFFRACTION5A148 - 166

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