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- PDB-8dwl: Inhibitor-3:PP1 coexpressed complex -

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Basic information

Entry
Database: PDB / ID: 8dwl
TitleInhibitor-3:PP1 coexpressed 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 / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion ...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 / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / 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 / 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 / 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 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
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: E3 ubiquitin-protein ligase PPP1R11
B: E3 ubiquitin-protein ligase PPP1R11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,44510
Polymers79,0594
Non-polymers3866
Water2,612145
1
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: E3 ubiquitin-protein ligase PPP1R11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6604
Polymers39,5292
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-83 kcal/mol
Surface area12980 Å2
MethodPISA
2
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
B: E3 ubiquitin-protein ligase PPP1R11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7846
Polymers39,5292
Non-polymers2554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-94 kcal/mol
Surface area13420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.343, 90.343, 196.332
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 / Fragment: UNP RESIDUES 7-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CA, PPP1A / Cell line (production host): expi293 / Production host: Homo sapiens (human)
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 / Cell line (production host): expi293 / Production host: Homo sapiens (human) / References: UniProt: O60927
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.1 M MES/imidazole pH 6.5, 0.03 M magnesium chloride, 0.03 M calcium chloride

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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: Oct 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2→39.57 Å / Num. obs: 55726 / % possible obs: 99.7 % / Redundancy: 8 % / Biso Wilson estimate: 40.44 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.05 / Rrim(I) all: 0.143 / Net I/σ(I): 8.4 / Num. measured all: 446561 / Scaling rejects: 31
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.054.23.0651642138920.3421.6263.4860.596.2
8.94-39.577.20.06153087420.9930.0240.06626.598.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MOV

4mov


Resolution: 2→38.92 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 31.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2372 3751 3.67 %
Rwork0.213 98498 -
obs0.2139 54457 97.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 191.06 Å2 / Biso mean: 53.6259 Å2 / Biso min: 25.11 Å2
Refinement stepCycle: final / Resolution: 2→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5137 0 12 145 5294
Biso mean--68.96 49 -
Num. residues----641
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.020.3994910.44032355244663
2.02-2.050.4451090.41232991310080
2.05-2.080.39811310.38763423355492
2.08-2.110.34181350.36863666380198
2.11-2.140.41561380.35713725386399
2.14-2.170.34121390.331537243863100
2.17-2.210.32431490.329637653914100
2.21-2.250.34431430.308137323875100
2.25-2.290.31591440.296637253869100
2.29-2.330.30431400.28437203860100
2.33-2.380.3371420.274337913933100
2.38-2.430.34541400.270437303870100
2.43-2.490.30481450.256337493894100
2.49-2.550.26811430.25337493892100
2.55-2.620.32151400.249737253865100
2.62-2.70.30381420.254137333875100
2.7-2.780.25341460.244437393885100
2.78-2.880.26361440.249337843928100
2.88-30.3491480.230937283876100
3-3.130.2941390.227637473886100
3.13-3.30.21751440.219137363880100
3.3-3.510.23281420.204637293871100
3.51-3.780.18171450.186737713916100
3.78-4.160.18071420.163837343876100
4.16-4.760.18181380.141337613899100
4.76-5.990.15631460.169737493895100
5.99-38.920.17631460.156937173863100

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