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- PDB-1b3u: CRYSTAL STRUCTURE OF CONSTANT REGULATORY DOMAIN OF HUMAN PP2A, PR... -

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Basic information

Entry
Database: PDB / ID: 1b3u
TitleCRYSTAL STRUCTURE OF CONSTANT REGULATORY DOMAIN OF HUMAN PP2A, PR65ALPHA
ComponentsPROTEIN (PROTEIN PHOSPHATASE PP2A)
KeywordsSCAFFOLD PROTEIN / PP2A / PHOSPHORYLATION / HEAT REPEAT
Function / homology
Function and homology information


meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / MASTL Facilitates Mitotic Progression / regulation of meiotic cell cycle process involved in oocyte maturation / mitotic sister chromatid separation / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / FAR/SIN/STRIPAK complex / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism ...meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / MASTL Facilitates Mitotic Progression / regulation of meiotic cell cycle process involved in oocyte maturation / mitotic sister chromatid separation / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / FAR/SIN/STRIPAK complex / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / female meiotic nuclear division / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / protein antigen binding / 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 / Initiation of Nuclear Envelope (NE) Reformation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / ERKs are inactivated / 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 / regulation of growth / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Co-inhibition by CTLA4 / protein serine/threonine phosphatase activity / Platelet sensitization by LDL / ERK/MAPK targets / T cell homeostasis / regulation of cell differentiation / chromosome, centromeric region / DARPP-32 events / lateral plasma membrane / negative regulation of hippo signaling / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin A/B1/B2 associated events during G2/M transition / 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 / Recruitment of NuMA to mitotic centrosomes / Resolution of Sister Chromatid Cohesion / Anchoring of the basal body to the plasma membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / AURKA Activation by TPX2 / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / chromosome segregation / RHO GTPases Activate Formins / RAF activation / Spry regulation of FGF signaling / Degradation of beta-catenin by the destruction complex / PKR-mediated signaling / Negative regulation of MAPK pathway / Separation of Sister Chromatids / Cyclin D associated events in G1 / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / Regulation of TP53 Degradation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein-containing complex assembly / intracellular signal transduction / neuron projection / protein heterodimerization activity / neuronal cell body / dendrite / glutamatergic synapse / mitochondrion / extracellular exosome / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / HEAT repeat / HEAT repeat / : / PPP2R1A-like HEAT repeat / HEAT repeat profile. / HEAT, type 2 / HEAT repeats / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant ...: / HEAT repeat / HEAT repeat / : / PPP2R1A-like HEAT repeat / HEAT repeat profile. / HEAT, type 2 / HEAT repeats / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.3 Å
AuthorsGroves, M.R. / Hanlon, N. / Turowski, P. / Hemmings, B. / Barford, D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: The structure of the protein phosphatase 2A PR65/A subunit reveals the conformation of its 15 tandemly repeated HEAT motifs.
Authors: Groves, M.R. / Hanlon, N. / Turowski, P. / Hemmings, B.A. / Barford, D.
History
DepositionDec 14, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Apr 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (PROTEIN PHOSPHATASE PP2A)
B: PROTEIN (PROTEIN PHOSPHATASE PP2A)


Theoretical massNumber of molelcules
Total (without water)130,4942
Polymers130,4942
Non-polymers00
Water13,133729
1
A: PROTEIN (PROTEIN PHOSPHATASE PP2A)


Theoretical massNumber of molelcules
Total (without water)65,2471
Polymers65,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (PROTEIN PHOSPHATASE PP2A)


Theoretical massNumber of molelcules
Total (without water)65,2471
Polymers65,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.280, 112.150, 122.630
Angle α, β, γ (deg.)90.00, 95.60, 90.00
Int Tables number4
Cell settingorthorhombic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999932, -0.011239, 0.003138), (0.010826, -0.793178, 0.608894), (-0.004354, 0.608886, 0.793246)
Vector: 174.44279, -1.514, 0.7045)

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Components

#1: Protein PROTEIN (PROTEIN PHOSPHATASE PP2A)


Mass: 65247.148 Da / Num. of mol.: 2 / Fragment: 65 KD REGULATORY SUBUNIT
Source method: isolated from a genetically manipulated source
Details: ALPHA ISOFORM / Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET28-M / Cell line (production host): B834 / Production host: Escherichia coli (E. coli) / References: UniProt: P30153
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 729 / 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: 2.5 Å3/Da / Density % sol: 64 %
Crystal growpH: 5.5 / Details: pH 5.5
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CITRATE11
2PEG 400011
3NACL11
4DTT11
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 %(w/v)PEG40001reservoir
2100 mMsodium citrate1reservoir
31
41

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Aug 1, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 63661 / % possible obs: 82.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 8.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 7.2 / Rsym value: 0.097 / % possible all: 40.3
Reflection shell
*PLUS
% possible obs: 40.3 % / Num. unique obs: 4473

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Processing

Software
NameVersionClassification
CNS0.4refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.3→25 Å / Rfactor Rfree error: 0.008 / Data cutoff high rms absF: 1948906.6 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1005 1.3 %THIN SHELLS
Rwork0.2092 ---
all-63584 --
obs-63584 82.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.85 Å2 / ksol: 0.309 e/Å3
Displacement parametersBiso mean: 41.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.59 Å20 Å21.47 Å2
2--3.78 Å20 Å2
3---1.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9140 0 0 729 9869
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d18.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.78
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 67 1.3 %
Rwork0.22 5263 -
obs--41.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAM
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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