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- PDB-6iur: A phosphatase complex STRN3-PP2Aa -

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Basic information

Entry
Database: PDB / ID: 6iur
TitleA phosphatase complex STRN3-PP2Aa
Components
  • PP2A scaffolding subunit
  • Striatin-3
KeywordsPROTEIN BINDING / Phosphatase / Complex
Function / homology
Function and homology information


armadillo repeat domain binding / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / mitotic sister chromatid separation / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / regulation of meiotic cell cycle process involved in oocyte maturation / meiotic sister chromatid cohesion, centromeric / INTAC complex ...armadillo repeat domain binding / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / mitotic sister chromatid separation / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / regulation of meiotic cell cycle process involved in oocyte maturation / meiotic sister chromatid cohesion, centromeric / INTAC complex / FAR/SIN/STRIPAK complex / negative regulation of intracellular estrogen receptor signaling pathway / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / female meiotic nuclear division / protein phosphatase regulator activity / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / protein antigen binding / ERKs are inactivated / Initiation of Nuclear Envelope (NE) Reformation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / RNA polymerase II transcription initiation surveillance / Co-stimulation by CD28 / regulation of growth / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Co-inhibition by CTLA4 / Platelet sensitization by LDL / ERK/MAPK targets / protein serine/threonine phosphatase activity / T cell homeostasis / regulation of cell differentiation / lateral plasma membrane / chromosome, centromeric region / DARPP-32 events / negative regulation of hippo signaling / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Cyclin A/B1/B2 associated events during G2/M transition / spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / protein phosphatase 2A binding / AURKA Activation by TPX2 / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / Spry regulation of FGF signaling / chromosome segregation / Degradation of beta-catenin by the destruction complex / RHO GTPases Activate Formins / RAF activation / PKR-mediated signaling / small GTPase binding / Negative regulation of MAPK pathway / Cyclin D associated events in G1 / Separation of Sister Chromatids / Regulation of TP53 Degradation / Regulation of PLK1 Activity at G2/M Transition / response to estradiol / microtubule cytoskeleton / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein-containing complex assembly / protein-macromolecule adaptor activity / calmodulin binding / neuron projection / postsynapse / intracellular signal transduction / protein heterodimerization activity / neuronal cell body / negative regulation of DNA-templated transcription / dendrite / chromatin / protein-containing complex binding / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / Golgi apparatus / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Striatin, N-terminal / : / Striatin family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / : / HEAT repeat / HEAT repeat / : / PPP2R1A-like HEAT repeat / HEAT repeat profile. ...Striatin, N-terminal / : / Striatin family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / : / HEAT repeat / HEAT repeat / : / PPP2R1A-like HEAT repeat / HEAT repeat profile. / HEAT, type 2 / HEAT repeats / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Armadillo-like helical / Alpha Horseshoe / 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 / Mainly Alpha
Similarity search - Domain/homology
PROPANE / Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / Striatin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.33 Å
AuthorsTang, Y. / Zhou, Z.C.
CitationJournal: Cancer Cell / Year: 2020
Title: Selective Inhibition of STRN3-Containing PP2A Phosphatase Restores Hippo Tumor-Suppressor Activity in Gastric Cancer.
Authors: Tang, Y. / Fang, G. / Guo, F. / Zhang, H. / Chen, X. / An, L. / Chen, M. / Zhou, L. / Wang, W. / Ye, T. / Zhou, L. / Nie, P. / Yu, H. / Lin, M. / Zhao, Y. / Lin, X. / Yuan, Z. / Jiao, S. / Zhou, Z.
History
DepositionNov 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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: PP2A scaffolding subunit
B: PP2A scaffolding subunit
C: Striatin-3
D: Striatin-3
E: PP2A scaffolding subunit
F: PP2A scaffolding subunit
G: Striatin-3
H: Striatin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,38914
Polymers285,1258
Non-polymers2656
Water905
1
A: PP2A scaffolding subunit
B: PP2A scaffolding subunit
C: Striatin-3
D: Striatin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,6516
Polymers142,5624
Non-polymers882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: PP2A scaffolding subunit
F: PP2A scaffolding subunit
G: Striatin-3
H: Striatin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,7398
Polymers142,5624
Non-polymers1764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.094, 201.743, 116.055
Angle α, β, γ (deg.)90.00, 106.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PP2A scaffolding subunit


Mass: 65264.219 Da / Num. of mol.: 4 / Fragment: UNP residues 8-589
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R1A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): CodonPlus / References: UniProt: P30153
#2: Protein/peptide
Striatin-3


Mass: 6016.993 Da / Num. of mol.: 4 / Fragment: UNP residues 86-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STRN3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): CodonPlus / References: UniProt: Q13033
#3: Chemical
ChemComp-TME / PROPANE


Mass: 44.096 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 4.28 Å3/Da / Density % sol: 71.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1M BIS-TRIS propane pH 9.0, 8.5% PEG20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.33→50 Å / Num. obs: 67955 / % possible obs: 99 % / Redundancy: 3 % / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.081 / Rrim(I) all: 0.142 / Net I/σ(I): 12.46
Reflection shellResolution: 3.33→3.449 Å / Rmerge(I) obs: 1.283 / Num. unique obs: 3368 / Rpim(I) all: 0.897 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I5L

4i5l


Resolution: 3.33→44.068 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2493 1834 2.96 %
Rwork0.1991 --
obs0.2005 61958 89.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.33→44.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19518 0 18 5 19541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00419812
X-RAY DIFFRACTIONf_angle_d0.86426854
X-RAY DIFFRACTIONf_dihedral_angle_d14.4212283
X-RAY DIFFRACTIONf_chiral_restr0.0463212
X-RAY DIFFRACTIONf_plane_restr0.0063447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3303-3.42030.43721130.35043635X-RAY DIFFRACTION71
3.4203-3.52090.39461260.33054088X-RAY DIFFRACTION80
3.5209-3.63450.34431240.29644321X-RAY DIFFRACTION84
3.6345-3.76440.32991490.25754633X-RAY DIFFRACTION90
3.7644-3.9150.29011390.22854620X-RAY DIFFRACTION90
3.915-4.09310.26171410.21114629X-RAY DIFFRACTION90
4.0931-4.30870.27241470.19494655X-RAY DIFFRACTION91
4.3087-4.57840.24021390.18354863X-RAY DIFFRACTION95
4.5784-4.93140.21961490.1664863X-RAY DIFFRACTION94
4.9314-5.42690.24511550.18054870X-RAY DIFFRACTION94
5.4269-6.21030.24911480.2174906X-RAY DIFFRACTION95
6.2103-7.81720.24131510.20414954X-RAY DIFFRACTION96
7.8172-44.0720.16751530.13885087X-RAY DIFFRACTION97
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)
12.95710.9078-0.16582.11781.97942.3299-0.07180.0469-0.2596-0.0026-0.5423-0.10180.8973-0.51350.46241.1584-0.072-0.30020.49590.09830.6434188.3987-0.1412157.2075
21.7946-0.0821-1.99221.7006-1.69878.86190.103-0.0629-0.2681-0.46680.1191-0.04260.29590.5123-0.36710.9757-0.1042-0.24250.68650.0480.5566195.6969-1.2844158.2424
31.9404-1.0288-0.0376.37981.38172.25870.17750.2454-0.13080.0343-0.35650.49810.1988-0.04910.15820.41180.1038-0.02670.6093-0.03540.5407156.0616-19.7376148.9505
45.32872.1861-2.54642.496-1.29551.68920.0490.27550.3713-0.0247-0.08280.4689-0.5741-0.2058-0.06420.7520.0972-0.07910.5581-0.05480.6991170.510116.8806147.3502
56.2495-1.89440.9752.64871.03081.62340.33490.8265-0.5119-0.14190.03-0.36260.35020.6599-0.43030.86320.1443-0.12240.79060.04550.6891216.28567.6132133.1446
61.4929-1.196-0.26747.91612.52583.53870.08930.33350.0524-0.5028-0.2819-0.0162-0.2264-0.17980.16240.4767-0.09680.00420.7114-0.05040.3774171.2976-54.902117.7119
72.7133-0.69161.50742.3569-1.05742.2070.4639-0.5679-0.54130.2624-0.33190.01110.5313-0.169-0.17120.9944-0.2805-0.04120.8029-0.00140.6107183.0266-93.1263128.1377
82.87812.6660.84023.01541.26134.0950.8343-0.66880.36840.8248-0.41550.24930.9987-1.1023-0.26761.0045-0.2821-0.04881.49320.27530.835202.0654-81.5806175.1865
93.71872.75064.553.25892.78665.8267-1.04790.22850.477-0.0960.4531-0.3942-0.6230.26060.68480.74130.0219-0.14860.5999-0.02540.6034179.3414-40.1705142.4357
102.5988-1.19973.0872.1749-1.00284.97290.24080.86150.15160.1743-0.2592-0.2367-0.08910.60840.03890.6772-0.0284-0.1930.6581-0.05210.6863181.89-38.9611135.4839
112.522.62930.96968.5481.71811.39470.2685-0.2769-0.21360.3025-0.2619-0.33520.2449-0.0422-0.00260.4613-0.092-0.09960.62610.01270.4476209.670619.0922175.6704
123.816-2.2672.23132.9388-3.08524.05530.02160.10780.2350.157-0.1353-0.1142-0.2108-0.18270.07750.5284-0.0721-0.01260.5351-0.15560.599205.228653.812160.9
131.69741.47161.29283.64953.05473.8452-0.07370.05460.0239-0.1011-0.10420.2040.0312-0.33310.16910.6120.12630.0550.7119-0.0340.6016170.075145.1593128.0962
141.84052.5289-0.9486.7176-1.90431.521-0.0339-0.07330.22220.3262-0.19950.1591-0.40670.12020.1750.53-0.0893-0.02640.510.04540.4661174.6078-19.0754176.9908
153.4825-1.9186-2.33933.54443.5763.6625-0.0657-0.3228-0.39380.3222-0.00450.17720.39290.2457-0.01710.6689-0.00070.07850.57210.11430.5975178.0789-54.3038166.1951
162.68680.1433-0.75962.487-1.51488.1971-0.08430.6350.1083-0.1899-0.3784-0.4028-0.18860.84870.46190.5080.1126-0.11860.78130.08480.6463206.3333-54.8772135.0252
171.82322.1841-1.11972.9839-1.14680.8058-1.28482.28171.2155-1.09650.98550.1239-2.8731.92150.82611.9903-0.8728-0.41292.19720.52141.4234223.2922-37.3295113.9038
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 84:130 )C84 - 130
2X-RAY DIFFRACTION2( CHAIN D AND RESID 86:131 )D86 - 131
3X-RAY DIFFRACTION3( CHAIN E AND RESID 7:195 )E7 - 195
4X-RAY DIFFRACTION4( CHAIN E AND RESID 196:365 )E196 - 365
5X-RAY DIFFRACTION5( CHAIN E AND RESID 366:587 )E366 - 587
6X-RAY DIFFRACTION6( CHAIN F AND RESID 7:140 )F7 - 140
7X-RAY DIFFRACTION7( CHAIN F AND RESID 141:395 )F141 - 395
8X-RAY DIFFRACTION8( CHAIN F AND RESID 396:588 )F396 - 588
9X-RAY DIFFRACTION9( CHAIN G AND RESID 85:130 )G85 - 130
10X-RAY DIFFRACTION10( CHAIN H AND RESID 86:131 )H86 - 131
11X-RAY DIFFRACTION11( CHAIN A AND RESID 8:174 )A8 - 174
12X-RAY DIFFRACTION12( CHAIN A AND RESID 175:348 )A175 - 348
13X-RAY DIFFRACTION13( CHAIN A AND RESID 349:588 )A349 - 588
14X-RAY DIFFRACTION14( CHAIN B AND RESID 7:174 )B7 - 174
15X-RAY DIFFRACTION15( CHAIN B AND RESID 175:333 )B175 - 333
16X-RAY DIFFRACTION16( CHAIN B AND RESID 334:513 )B334 - 513
17X-RAY DIFFRACTION17( CHAIN B AND RESID 514:587 )B514 - 587

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