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- PDB-3egg: Crystal structure of a complex between Protein Phosphatase 1 alph... -

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Basic information

Entry
Database: PDB / ID: 3egg
TitleCrystal structure of a complex between Protein Phosphatase 1 alpha (PP1) and the PP1 binding and PDZ domains of Spinophilin
Components
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
  • Spinophilin
KeywordsHYDROLASE / PP1 / Spinophilin / Serine/Threonine Phosphatase / Post Synaptic Density / Glutametergic Receptors / Carbohydrate metabolism / Cell cycle / Cell division / Glycogen metabolism / Iron / Manganese / Metal-binding / Phosphoprotein / Protein phosphatase / Actin-binding / Cell junction / Cell projection / Cytoskeleton / Developmental protein / Differentiation / Neurogenesis / Nucleus / Synapse
Function / homology
Function and homology information


protein localization to actin cytoskeleton / positive regulation of protein localization to actin cortical patch / response to L-phenylalanine derivative / protein localization to cell periphery / cytoplasmic side of dendritic spine plasma membrane / cellular response to morphine / spine apparatus / regulation of opioid receptor signaling pathway / extrinsic component of postsynaptic membrane / developmental process involved in reproduction ...protein localization to actin cytoskeleton / positive regulation of protein localization to actin cortical patch / response to L-phenylalanine derivative / protein localization to cell periphery / cytoplasmic side of dendritic spine plasma membrane / cellular response to morphine / spine apparatus / regulation of opioid receptor signaling pathway / extrinsic component of postsynaptic membrane / developmental process involved in reproduction / regulation of glycogen catabolic process / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / response to kainic acid / glycogen granule / RNA polymerase II promoter clearance / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / cellular response to peptide / cadherin binding involved in cell-cell adhesion / protein phosphatase 1 binding / regulation of translational initiation in response to stress / filopodium assembly / actin filament depolymerization / reproductive system development / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / dendritic spine membrane / dephosphorylation / response to steroid hormone / regulation of canonical Wnt signaling pathway / dendritic spine neck / protein phosphatase inhibitor activity / dendritic spine head / glycogen metabolic process / cortical actin cytoskeleton / male mating behavior / protein-serine/threonine phosphatase / branching morphogenesis of an epithelial tube / Triglyceride catabolism / entrainment of circadian clock by photoperiod / Maturation of hRSV A proteins / protein serine/threonine phosphatase activity / dendrite development / response to immobilization stress / phosphatase activity / telomere maintenance in response to DNA damage / phosphoprotein phosphatase activity / negative regulation of transcription elongation by RNA polymerase II / transition metal ion binding / regulation of postsynapse assembly / DARPP-32 events / positive regulation of glycogen biosynthetic process / response to amino acid / ribonucleoprotein complex binding / protein dephosphorylation / D2 dopamine receptor binding / positive regulation of protein localization / response to prostaglandin E / lung development / cellular response to epidermal growth factor stimulus / actin filament organization / response to amphetamine / Downregulation of TGF-beta receptor signaling / learning / response to nicotine / positive regulation of protein localization to plasma membrane / hippocampus development / filopodium / adherens junction / circadian regulation of gene expression / cellular response to estradiol stimulus / positive regulation of transcription elongation by RNA polymerase II / calcium-mediated signaling / negative regulation of cell growth / regulation of circadian rhythm / cerebral cortex development / response to lead ion / kinase binding / ruffle membrane / cellular response to xenobiotic stimulus / neuron projection development / actin filament binding / : / cell migration / response to estradiol / presynapse / lamellipodium / actin cytoskeleton / actin binding / growth cone / perikaryon / dendritic spine / nucleic acid binding / transmembrane transporter binding / protein kinase activity / postsynaptic density / protein stabilization / iron ion binding / response to xenobiotic stimulus / cell division
Similarity search - Function
Neurabin-1/2, PDZ domain / Neurabin-like family / PDZ domain / 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 ...Neurabin-1/2, PDZ domain / Neurabin-like family / PDZ domain / 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 / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / 4-Layer Sandwich / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Neurabin-2 / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsRagusa, M.J. / Page, R. / Peti, W.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Spinophilin directs protein phosphatase 1 specificity by blocking substrate binding sites.
Authors: Ragusa, M.J. / Dancheck, B. / Critton, D.A. / Nairn, A.C. / Page, R. / Peti, W.
History
DepositionSep 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
C: Spinophilin
D: Spinophilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,39518
Polymers111,9454
Non-polymers1,45014
Water9,386521
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
C: Spinophilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6469
Polymers55,9722
Non-polymers6737
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-14 kcal/mol
Surface area19690 Å2
MethodPISA
2
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: Spinophilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7499
Polymers55,9722
Non-polymers7777
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-16 kcal/mol
Surface area15140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.675, 84.418, 109.164
Angle α, β, γ (deg.)90.000, 93.500, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-476-

HOH

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / PP-1A


Mass: 37349.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CA, PPP1A / Plasmid: RP1B / Production host: Escherichia coli (E. coli)
References: UniProt: P62136, protein-serine/threonine phosphatase
#2: Protein Spinophilin / Neurabin-II / Neurabin-2 / Protein phosphatase 1 regulatory subunit 9B / Neural tissue-specific F- ...Neurabin-II / Neurabin-2 / Protein phosphatase 1 regulatory subunit 9B / Neural tissue-specific F-actin-binding protein II / p130 / PP1bp134


Mass: 18622.635 Da / Num. of mol.: 2 / Fragment: PP1 binding and PDZ domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ppp1r9b / Plasmid: RP1B / Production host: Escherichia coli (E. coli) / References: UniProt: O35274

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Non-polymers , 4 types, 535 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M NaCl, 0.1M MES, 10% PEG 4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 20, 2008
Details: Double crystal channel cut, Si(111), 1m long Rh coated toroidal mirror for vertical and horizontal focusing
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 92215 / Num. obs: 91570 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 22.26 Å2 / Rsym value: 0.078 / Χ2: 1.052
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.98 / Num. unique all: 4508 / Rsym value: 0.596 / Χ2: 0.918 / % possible all: 97.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 43.72 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å27.53 Å
Translation2.5 Å27.53 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3E7A and 2G5M

3e7a

2g5m


Resolution: 1.85→27.53 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.214 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.873 / SU B: 4.642 / SU ML: 0.073 / SU R Cruickshank DPI: 0.139 / SU Rfree: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.211 4548 5 %RANDOM
Rwork0.179 ---
obs0.181 87003 99.09 %-
all-87802 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.82 Å2 / Biso mean: 25.775 Å2 / Biso min: 11.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.98 Å2
2--0.51 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.85→27.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6349 0 82 521 6952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226641
X-RAY DIFFRACTIONr_angle_refined_deg1.2611.9838986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8485822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70324.161310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.992151116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7391542
X-RAY DIFFRACTIONr_chiral_restr0.0970.2984
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025036
X-RAY DIFFRACTIONr_nbd_refined0.1970.23105
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24548
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2485
X-RAY DIFFRACTIONr_metal_ion_refined0.0280.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.223
X-RAY DIFFRACTIONr_mcbond_it0.621.54198
X-RAY DIFFRACTIONr_mcangle_it0.97426558
X-RAY DIFFRACTIONr_scbond_it1.74132765
X-RAY DIFFRACTIONr_scangle_it2.6454.52422
LS refinement shellResolution: 1.85→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 330 -
Rwork0.246 6136 -
all-6466 -
obs-6136 95.05 %
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)
19.9372-4.7947.22085.4032-6.68913.61920.04680.29140.3203-0.1827-0.0578-0.1336-0.19140.17130.011-0.0787-0.07210.0189-0.11440.0115-0.0840.1805-15.5042-17.2308
23.43260.695-2.75941.4523-1.24245.755-0.1831-0.0764-0.2154-0.07320.0298-0.06380.29220.15250.1533-0.1579-0.0279-0.0201-0.1792-0.0208-0.1335-4.3895-29.3911-8.8086
31.8860.1753-0.43390.9534-0.11041.5328-0.08250.1387-0.0323-0.05110.03620.11920.1288-0.26930.0463-0.1348-0.0274-0.0141-0.1105-0.0107-0.1369-16.4198-27.5318-10.6108
42.26510.4187-0.72142.6104-0.63262.4223-0.02280.18690.17590.00340.04230.3376-0.0771-0.5134-0.0195-0.15840.0055-0.02520.0223-0.0147-0.0279-29.6729-21.324-6.5371
52.5053-0.52662.01932.8436-2.442814.337-0.0083-0.01250.45140.137-0.0630.1156-0.62360.19840.0713-0.08740.0621-0.0086-0.0807-0.01790.0582-21.0075-10.279-4.0118
610.43042.06613.61613.02931.80929.3068-0.03310.14050.3263-0.03250.03310.4317-0.2363-0.46950-0.08050.06920.0201-0.04990.0316-0.04112.8396-16.1446-37.0248
71.51920.2671-0.70711.4418-0.06561.7112-0.0085-0.04010.08130.01750.02470.0776-0.0165-0.1042-0.0162-0.13470.0080.0013-0.1499-0.0038-0.14913.9971-23.0067-39.9975
81.83740.1183-0.90281.370.22011.7704-0.05410.0054-0.2182-0.0366-0.0093-0.10680.16490.01920.0633-0.08870.0146-0.0049-0.1589-0.0016-0.135624.7806-33.3973-48.3273
91.6445-0.0623-0.24222.64960.5451.9578-0.0058-0.0715-0.0298-0.0280.0269-0.21910.0020.2272-0.0211-0.14160.00130.0063-0.1425-0.0014-0.106834.3928-23.1643-48.1205
102.85320.35180.96052.3968-0.121212.78940.1193-0.08280.1496-0.0453-0.00110.0301-0.2456-0.1377-0.1182-0.1133-0.03040.0308-0.1853-0.0075-0.071226.8993-10.7116-45.3349
1110.36710.9898-3.86082.93851.05812.15350.2912-0.1890.3419-0.1799-0.2197-0.0375-0.62550.3116-0.07150.10740.1262-0.08630.02390.0610.2392-20.8971-2.2014-10.6698
122.4119-0.3496-1.04992.69340.80514.63050.10810.0660.44030.04170.12090.2661-0.2282-0.4677-0.229-0.12730.0641-0.0764-0.06640.01680.0835-23.7428-9.5846-6.2713
131.1922-3.4414-1.838817.00536.00922.9057-0.13970.40220.0049-0.6216-0.03310.474-0.4892-0.82190.17290.1434-0.1095-0.06280.2377-0.024-0.0396-18.8275-31.2383-30.6222
145.35020.3112-0.43082.2015-0.46671.255-0.067-0.2833-0.62270.1708-0.1486-0.06170.0340.22350.21560.1954-0.0392-0.01350.0780.0210.1497-5.2723-49.4945-37.1442
156.80120.2757-0.54531.10470.03770.8826-0.04990.0803-0.63390.036-0.0155-0.20820.14460.22250.06540.1101-0.0287-0.02630.05930.0320.0392-4.5383-48.2012-40.8594
1611.56036.1522-31.914312.4414-17.177688.10941.392-0.20511.09120.89180.56430.8676-1.5249-1.0817-1.95630.1570.01150.04090.1511-0.07550.177714.9218-1.2639-29.5577
1715.3351-2.667-8.92111.59644.652712.62180.19190.8068-0.0683-0.5707-0.1418-0.6739-0.1767-0.1645-0.0501-0.0034-0.0408-0.0239-0.10910.0523-0.017935.1152-4.1072-52.1215
182.25350.7703-1.79351.8137-1.59725.02160.1470.03490.20870.0760.0423-0.0232-0.0330.0195-0.1893-0.1196-0.0029-0.0142-0.16950.0029-0.050227.3247-8.982-45.1727
191.81.9694-1.952725.396-2.89332.1430.0249-0.2166-0.26410.8593-0.1773-0.03510.38430.17740.15240.15750.0431-0.0770.12650.0402-0.016122.622-36.633-24.5171
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 267 - 26
2X-RAY DIFFRACTION2AA27 - 5627 - 56
3X-RAY DIFFRACTION3AA57 - 22457 - 224
4X-RAY DIFFRACTION4AA225 - 279225 - 279
5X-RAY DIFFRACTION5AA280 - 300280 - 300
6X-RAY DIFFRACTION6BB7 - 207 - 20
7X-RAY DIFFRACTION7BB21 - 14521 - 145
8X-RAY DIFFRACTION8BB146 - 216146 - 216
9X-RAY DIFFRACTION9BB217 - 274217 - 274
10X-RAY DIFFRACTION10BB275 - 300275 - 300
11X-RAY DIFFRACTION11CC424 - 44011 - 27
12X-RAY DIFFRACTION12CC441 - 46928 - 56
13X-RAY DIFFRACTION13CC470 - 48357 - 70
14X-RAY DIFFRACTION14CC484 - 51671 - 103
15X-RAY DIFFRACTION15CC517 - 583104 - 170
16X-RAY DIFFRACTION16DD424 - 43011 - 17
17X-RAY DIFFRACTION17DD431 - 44318 - 30
18X-RAY DIFFRACTION18DD444 - 46931 - 56
19X-RAY DIFFRACTION19DD470 - 48957 - 76

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