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- PDB-1u32: Crystal structure of a Protein Phosphatase-1: Calcineurin Hybrid ... -

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Entry
Database: PDB / ID: 1u32
TitleCrystal structure of a Protein Phosphatase-1: Calcineurin Hybrid Bound to Okadaic Acid
ComponentsSerine/threonine protein phosphatase PP1-gamma catalytic subunit
KeywordsHYDROLASE
Function / homology
Function and homology information


PTW/PP1 phosphatase complex / regulation of nucleocytoplasmic transport / protein phosphatase 1 binding / lamin binding / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / 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 ...PTW/PP1 phosphatase complex / regulation of nucleocytoplasmic transport / protein phosphatase 1 binding / lamin binding / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / 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 / glycogen metabolic process / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / Triglyceride catabolism / entrainment of circadian clock by photoperiod / Maturation of hRSV A proteins / phosphatase activity / microtubule organizing center / cleavage furrow / mitotic sister chromatid segregation / phosphoprotein phosphatase activity / blastocyst development / protein dephosphorylation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / positive regulation of glial cell proliferation / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / Downregulation of TGF-beta receptor signaling / RHO GTPases Activate Formins / RAF activation / circadian regulation of gene expression / regulation of circadian rhythm / kinetochore / neuron differentiation / Separation of Sister Chromatids / : / MAPK cascade / presynapse / midbody / spermatogenesis / dendritic spine / mitochondrial outer membrane / nuclear speck / protein domain specific binding / cell division / focal adhesion / protein-containing complex binding / protein kinase binding / nucleolus / glutamatergic synapse / protein-containing complex / mitochondrion / RNA binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase ...Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / : / OKADAIC ACID / Serine/threonine-protein phosphatase PP1-gamma catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMaynes, J.T. / Perreault, K.R. / Cherney, M.M. / Luu, H.A. / James, M.N.G. / Holmes, C.F.B.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure and Mutagenesis of a Protein Phosphatase-1:Calcineurin Hybrid Elucidate the Role of the {beta}12-{beta}13 Loop in Inhibitor Binding
Authors: Maynes, J.T. / Perreault, K.R. / Cherney, M.M. / Luu, H.A. / James, M.N.G. / Holmes, C.F.B.
History
DepositionJul 20, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine protein phosphatase PP1-gamma catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9217
Polymers33,7721
Non-polymers1,1496
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.759, 98.759, 62.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Serine/threonine protein phosphatase PP1-gamma catalytic subunit / Protein Phosphatase-1: Calcineurin hybrid / PP-1G / Protein phosphatase 1C catalytic subunit


Mass: 33771.910 Da / Num. of mol.: 1 / Fragment: residues 6-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CC / Plasmid: pet / Production host: Escherichia coli (E. coli)
References: UniProt: P36873, protein-serine/threonine phosphatase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-OKA / OKADAIC ACID / 9,10-DEEPITHIO-9,10-DIDEHYDROACANTHIFOLICIN


Mass: 805.003 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H68O13 / Comment: toxin*YM
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.4 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: lithium sulfate, tris, PEG 400, mercaptoethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 22, 2002 / Details: osmic mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 21891 / Num. obs: 21304 / % possible obs: 97.3 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 2.5 / Redundancy: 5.8 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.057 / Net I/σ(I): 21.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 5.02 / Num. unique all: 2063 / Rsym value: 0.36 / % possible all: 99

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1JK7

1jk7


Resolution: 2→36.01 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1946384.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1250 5.9 %RANDOM
Rwork0.218 ---
all0.22 21272 --
obs0.218 21272 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.2487 Å2 / ksol: 0.359391 e/Å3
Displacement parametersBiso mean: 27.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2→36.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 71 89 2531
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.112
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 199 5.8 %
Rwork0.232 3254 -
obs--98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2BME.PARAMBME.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4DAM.PARAMDAM.TOP
X-RAY DIFFRACTION5WATER_REP.PARAMWATER.TOP

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