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- PDB-4ut3: X-ray structure of the human PP1 gamma catalytic subunit treated ... -

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Basic information

Entry
Database: PDB / ID: 4ut3
TitleX-ray structure of the human PP1 gamma catalytic subunit treated with hydrogen peroxide
Components(SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT) x 2
KeywordsHYDROLASE / METAL CENTER / METALLOPROTEIN / ENZYME ACTIVATION / PHOSPHOPROTEIN PHOSPHATASES / PROTEIN PHOSPHATASE 1
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 / glycogen metabolic process / protein-serine/threonine phosphatase / Triglyceride catabolism / entrainment of circadian clock by photoperiod ...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 / glycogen metabolic process / protein-serine/threonine phosphatase / Triglyceride catabolism / entrainment of circadian clock by photoperiod / Maturation of hRSV A proteins / protein serine/threonine phosphatase activity / phosphatase activity / cleavage furrow / microtubule organizing center / phosphoprotein phosphatase activity / mitotic sister chromatid segregation / blastocyst development / positive regulation of glial cell proliferation / protein dephosphorylation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / Downregulation of TGF-beta receptor signaling / circadian regulation of gene expression / RHO GTPases Activate Formins / RAF activation / regulation of circadian rhythm / kinetochore / neuron differentiation / Separation of Sister Chromatids / : / presynapse / MAPK cascade / midbody / spermatogenesis / dendritic spine / mitochondrial outer membrane / nuclear speck / protein domain specific binding / cell division / focal adhesion / protein kinase binding / protein-containing complex binding / nucleolus / glutamatergic synapse / protein-containing complex / mitochondrion / RNA binding / metal ion binding / nucleus / cytoplasm / cytosol
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
: / PHOSPHATE ION / Serine/threonine-protein phosphatase PP1-gamma catalytic subunit
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsZeh Silva, M. / Kopec, J. / Fotinou, D. / Steiner, R.A.
CitationJournal: Embo J. / Year: 2016
Title: Targeted Redox Inhibition of Protein Phosphatase 1 by Nox4 Regulates Eif2Alpha-Mediated Stress Signaling.
Authors: Santos, C.X. / Hafstad, A.D. / Beretta, M. / Zhang, M. / Molenaar, C. / Kopec, J. / Fotinou, D. / Murray, T.V. / Cobb, A.M. / Martin, D. / Zeh Silva, M. / Anilkumar, N. / Schroder, K. / ...Authors: Santos, C.X. / Hafstad, A.D. / Beretta, M. / Zhang, M. / Molenaar, C. / Kopec, J. / Fotinou, D. / Murray, T.V. / Cobb, A.M. / Martin, D. / Zeh Silva, M. / Anilkumar, N. / Schroder, K. / Shanahan, C.M. / Brewer, A.C. / Brandes, R.P. / Blanc, E. / Parsons, M. / Belousov, V. / Cammack, R. / Hider, R.C. / Steiner, R.A. / Shah, A.M.
History
DepositionJul 17, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references / Structure summary
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
B: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5198
Polymers74,1102
Non-polymers4106
Water2,900161
1
A: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2524
Polymers37,0471
Non-polymers2053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2684
Polymers37,0631
Non-polymers2053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.450, 105.220, 89.820
Angle α, β, γ (deg.)90.00, 90.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT / PP-1G / PROTEIN PHOSPHATASE 1C CATALYTIC SUBUNIT / PROTEIN PHOSPHATASE 1 GAMMA ISOFORM


Mass: 37046.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI DH5[ALPHA] (bacteria)
References: UniProt: P36873, protein-serine/threonine phosphatase
#2: Protein SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT / PP-1G / PROTEIN PHOSPHATASE 1C CATALYTIC SUBUNIT / PROTEIN PHOSPHATASE 1 GAMMA ISOFORM


Mass: 37062.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI DH5[ALPHA] (bacteria)
References: UniProt: P36873, protein-serine/threonine phosphatase
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
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: 2.46 Å3/Da / Density % sol: 49.96 % / Description: NONE
Crystal growpH: 9
Details: 7-12% PEG3350, 0.1 M BICINE, PH 9.0 SOAKING IN RESERVOIR ENRICHED WITH 50MM H2O2 FOR 10 MINS CRYOPROTECTION IN RESEVOIR ENRICHED WITH 25% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.2→45.4 Å / Num. obs: 35328 / % possible obs: 97.5 % / Observed criterion σ(I): -1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.9
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.1 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O8A

2o8a


Resolution: 2.19→45.4 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.46 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21146 1742 4.9 %RANDOM
Rwork0.17336 ---
obs0.17518 33509 95.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.211 Å2
Baniso -1Baniso -2Baniso -3
1--32.79 Å20 Å2-4.58 Å2
2--46 Å20 Å2
3----13.21 Å2
Refinement stepCycle: LAST / Resolution: 2.19→45.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4745 0 14 161 4920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194879
X-RAY DIFFRACTIONr_bond_other_d0.0030.024640
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.9736583
X-RAY DIFFRACTIONr_angle_other_deg0.81310690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9555590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75123.967242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8715863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1181534
X-RAY DIFFRACTIONr_chiral_restr0.0740.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025480
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021154
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_it2.9184.3912354
X-RAY DIFFRACTIONr_mcbond_other2.9174.392353
X-RAY DIFFRACTIONr_mcangle_it4.3516.582940
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8824.9012525
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.189→2.246 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 114 -
Rwork0.315 1959 -
obs--75.6 %

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