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- PDB-8dwk: Inhibitor-3:PP1 reconstituted complex -

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Basic information

Entry
Database: PDB / ID: 8dwk
TitleInhibitor-3:PP1 reconstituted complex
Components
  • E3 ubiquitin-protein ligase PPP1R11
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE / Inhibitor-3 / Protein phosphatase 1
Function / homology
Function and homology information


regulation of glycogen catabolic process / protein serine/threonine phosphatase inhibitor activity / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / glycogen granule / RNA polymerase II promoter clearance / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / cadherin binding involved in cell-cell adhesion / protein phosphatase 1 binding ...regulation of glycogen catabolic process / protein serine/threonine phosphatase inhibitor activity / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / glycogen granule / RNA polymerase II promoter clearance / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / cadherin binding involved in cell-cell adhesion / protein phosphatase 1 binding / regulation of translational initiation in response to stress / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / dephosphorylation / regulation of canonical Wnt signaling pathway / negative regulation of cytokine production / protein phosphatase inhibitor activity / glycogen metabolic process / protein-serine/threonine phosphatase / branching morphogenesis of an epithelial tube / entrainment of circadian clock by photoperiod / Triglyceride catabolism / 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 / phosphatase binding / ribonucleoprotein complex binding / protein dephosphorylation / lung development / Downregulation of TGF-beta receptor signaling / adherens junction / circadian regulation of gene expression / positive regulation of transcription elongation by RNA polymerase II / regulation of circadian rhythm / RING-type E3 ubiquitin transferase / response to lead ion / ubiquitin protein ligase activity / : / presynapse / ubiquitin-dependent protein catabolic process / perikaryon / dendritic spine / defense response to Gram-positive bacterium / protein stabilization / protein ubiquitination / iron ion binding / cell division / nucleolus / glutamatergic synapse / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Type 1 protein phosphatase inhibitor / Protein phosphatase inhibitor / 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 ...Type 1 protein phosphatase inhibitor / Protein phosphatase inhibitor / 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
: / E3 ubiquitin-protein ligase PPP1R11 / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChoy, M.S. / Srivastava, G. / Page, R. / Peti, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM144483 United States
CitationJournal: Nat Commun / Year: 2023
Title: Inhibitor-3 inhibits Protein Phosphatase 1 via a metal binding dynamic protein-protein interaction.
Authors: Srivastava, G. / Choy, M.S. / Bolik-Coulon, N. / Page, R. / Peti, W.
History
DepositionAug 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 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

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: E3 ubiquitin-protein ligase PPP1R11
D: E3 ubiquitin-protein ligase PPP1R11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2798
Polymers79,0594
Non-polymers2204
Water99155
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
C: E3 ubiquitin-protein ligase PPP1R11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6394
Polymers39,5292
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-27 kcal/mol
Surface area12820 Å2
MethodPISA
2
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: E3 ubiquitin-protein ligase PPP1R11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6394
Polymers39,5292
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-26 kcal/mol
Surface area12870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.373, 91.373, 196.396
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 34162.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CA, PPP1A / Production host: Escherichia coli (E. coli)
References: UniProt: P62136, protein-serine/threonine phosphatase
#2: Protein/peptide E3 ubiquitin-protein ligase PPP1R11 / Hemochromatosis candidate gene V protein / HCG V / Protein phosphatase 1 regulatory subunit 11 / ...Hemochromatosis candidate gene V protein / HCG V / Protein phosphatase 1 regulatory subunit 11 / Protein phosphatase inhibitor 3


Mass: 5367.304 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1R11, HCGV, TCTE5 / Production host: Escherichia coli (E. coli) / References: UniProt: O60927
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.1 M bicine/Trizma base pH 8.5, 0.03 M diethyleneglycol, 0.03 M triethyleneglycol, 0.03 M tetraethyleneglycol, 0.03 M pentaethyleneglycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→39.28 Å / Num. obs: 29709 / % possible obs: 99.9 % / Redundancy: 12.1 % / Biso Wilson estimate: 48.62 Å2 / CC1/2: 0.996 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-IDRmerge(I) obs
2.5-2.632570.6511
9.01-39.287470.99910.051

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MOV

4mov


Resolution: 2.5→39.09 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 29.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 2765 5.05 %
Rwork0.2129 51977 -
obs0.2142 29512 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.36 Å2 / Biso mean: 58.4482 Å2 / Biso min: 24.98 Å2
Refinement stepCycle: final / Resolution: 2.5→39.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5080 0 4 55 5139
Biso mean--42.08 50.49 -
Num. residues----640
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.540.3171330.31662409254293
2.54-2.590.32341280.30052619274799
2.59-2.640.37331400.308225972737100
2.64-2.690.3241260.290226342760100
2.69-2.750.31181340.280326102744100
2.75-2.810.31641190.265826092728100
2.81-2.880.30881110.290726392750100
2.88-2.960.35481170.274326172734100
2.96-3.050.29561480.263726332781100
3.05-3.150.27331210.257826472768100
3.15-3.260.28661640.240825522716100
3.26-3.390.29471300.251126262756100
3.39-3.540.25411650.227825622727100
3.54-3.730.2481560.210826002756100
3.73-3.960.22751560.194925912747100
3.97-4.270.20711360.175926222758100
4.27-4.70.15281690.153825692738100
4.7-5.380.19481290.172526392768100
5.38-6.770.23331390.208626062745100
6.77-39.090.18511440.159325962740100

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