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- PDB-8sw6: Protein Phosphatase 1 in complex with PP1-specific Phosphatase ta... -

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Basic information

Entry
Database: PDB / ID: 8sw6
TitleProtein Phosphatase 1 in complex with PP1-specific Phosphatase targeting peptide (PhosTAP) version 3
Components
  • PP1-specific Phosphatase-Targeting Peptide version 3
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsBIOSYNTHETIC PROTEIN / Phosphatase-targeting peptide / complex / phosphatase regulator
Function / homology
Function and homology information


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 / RNA polymerase II promoter clearance / glycogen granule / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / regulation of translational initiation in response to stress / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity ...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 / RNA polymerase II promoter clearance / glycogen granule / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / regulation of translational initiation in response to stress / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / dephosphorylation / regulation of canonical Wnt signaling pathway / branching morphogenesis of an epithelial tube / 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 / telomere maintenance in response to DNA damage / phosphoprotein phosphatase activity / negative regulation of transcription elongation by RNA polymerase II / transition metal ion binding / DARPP-32 events / positive regulation of glycogen biosynthetic process / ribonucleoprotein complex binding / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / adherens junction / positive regulation of transcription elongation by RNA polymerase II / lung development / circadian regulation of gene expression / response to lead ion / regulation of circadian rhythm / : / presynapse / dendritic spine / perikaryon / protein stabilization / iron ion binding / cell division / nucleolus / glutamatergic synapse / extracellular exosome / nucleoplasm / nucleus / plasma membrane / 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 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
: / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsChoy, M.S. / Peti, W. / Page, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: A protein phosphatase 1 specific phos phatase ta rgeting p eptide (PhosTAP) to identify the PP1 phosphatome.
Authors: Choy, M.S. / Nguyen, H.T. / Kumar, G.S. / Peti, W. / Kettenbach, A.N. / Page, R.
History
DepositionMay 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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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-alpha catalytic subunit
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
C: PP1-specific Phosphatase-Targeting Peptide version 3
D: PP1-specific Phosphatase-Targeting Peptide version 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,70914
Polymers79,0954
Non-polymers61410
Water9,548530
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
C: PP1-specific Phosphatase-Targeting Peptide version 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9208
Polymers39,5472
Non-polymers3736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-77 kcal/mol
Surface area13290 Å2
MethodPISA
2
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: PP1-specific Phosphatase-Targeting Peptide version 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7896
Polymers39,5472
Non-polymers2414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-61 kcal/mol
Surface area12770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.004, 92.004, 199.581
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

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


Mass: 34162.148 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 7-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CA, PPP1A / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P62136, protein-serine/threonine phosphatase
#2: Protein/peptide PP1-specific Phosphatase-Targeting Peptide version 3


Mass: 5385.193 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 4 types, 540 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7
Details: 0.1 M HEPES, pH 7.0, 0.1 M lithium sulfate, 30% w/v polyvinylpyrrolidone

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.75→39.59 Å / Num. obs: 85929 / % possible obs: 98.7 % / Redundancy: 16.4 % / CC1/2: 0.968 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.019 / Rrim(I) all: 0.074 / Net I/σ(I): 21.9 / Num. measured all: 1407248
Reflection shellResolution: 1.75→1.78 Å / % possible obs: 97.2 % / Redundancy: 15.7 % / Rmerge(I) obs: 1.254 / Num. measured all: 69627 / Num. unique obs: 4425 / CC1/2: 0.939 / Rpim(I) all: 0.358 / Rrim(I) all: 1.315 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX1.19.1-4122refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→39.59 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2079 1659 2.05 %
Rwork0.1746 --
obs0.1753 80817 93.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→39.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5114 0 22 530 5666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085283
X-RAY DIFFRACTIONf_angle_d0.9517144
X-RAY DIFFRACTIONf_dihedral_angle_d13.7291961
X-RAY DIFFRACTIONf_chiral_restr0.058759
X-RAY DIFFRACTIONf_plane_restr0.007927
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.810.34441130.29245405X-RAY DIFFRACTION78
1.81-1.870.28671160.265481X-RAY DIFFRACTION79
1.87-1.930.25551180.22565457X-RAY DIFFRACTION79
1.93-2.010.27721420.20296805X-RAY DIFFRACTION98
2.01-2.10.26691440.19936902X-RAY DIFFRACTION99
2.1-2.210.21761440.19246882X-RAY DIFFRACTION99
2.21-2.350.23041410.19446810X-RAY DIFFRACTION98
2.35-2.530.2161470.1896956X-RAY DIFFRACTION99
2.53-2.790.20761460.18747015X-RAY DIFFRACTION99
2.79-3.190.22341450.18236929X-RAY DIFFRACTION98
3.19-4.020.18971490.15857148X-RAY DIFFRACTION100
4.02-39.590.17021540.14357368X-RAY DIFFRACTION98

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