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- PDB-8u5g: Crystal structure of the co-expressed SDS22:PP1:I3 complex -

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Basic information

Entry
Database: PDB / ID: 8u5g
TitleCrystal structure of the co-expressed SDS22:PP1:I3 complex
Components
  • E3 ubiquitin-protein ligase PPP1R11
  • Protein phosphatase 1 regulatory subunit 7
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE / Phosphatase / inhibitor
Function / homology
Function and homology information


protein serine/threonine phosphatase inhibitor 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 ...protein serine/threonine phosphatase inhibitor 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 / protein phosphatase regulator activity / 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 / negative regulation of cytokine production / protein phosphatase inhibitor activity / 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 / phosphatase binding / ribonucleoprotein complex binding / protein dephosphorylation / enzyme regulator activity / 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 / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / : / presynapse / chromosome / ubiquitin-dependent protein catabolic process / dendritic spine / perikaryon / defense response to Gram-positive bacterium / protein stabilization / protein ubiquitination / iron ion binding / cell division / nucleolus / glutamatergic synapse / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Type 1 protein phosphatase inhibitor / Protein phosphatase inhibitor / : / Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats ...Type 1 protein phosphatase inhibitor / Protein phosphatase inhibitor / : / Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / Leucine-rich repeat / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Leucine-rich repeat, SDS22-like subfamily / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
: / PHOSPHATE ION / E3 ubiquitin-protein ligase PPP1R11 / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / Protein phosphatase 1 regulatory subunit 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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: J.Biol.Chem. / Year: 2023
Title: The SDS22:PP1:I3 complex: SDS22 binding to PP1 loosens the active site metal to prime metal exchange.
Authors: Choy, M.S. / Srivastava, G. / Robinson, L.C. / Tatchell, K. / Page, R. / Peti, W.
History
DepositionSep 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 3, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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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: Protein phosphatase 1 regulatory subunit 7
C: E3 ubiquitin-protein ligase PPP1R11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,62214
Polymers75,6173
Non-polymers1,00611
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)334.795, 334.795, 334.795
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 34162.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CA, PPP1A / Plasmid: pcDNA3.4_K_RP1B / Cell line (production host): expi293 / Production host: Homo sapiens (human)
References: UniProt: P62136, protein-serine/threonine phosphatase
#2: Protein Protein phosphatase 1 regulatory subunit 7 / Protein phosphatase 1 regulatory subunit 22


Mass: 36087.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1R7, SDS22 / Plasmid: pcDNA3.4_K_RP1B / Cell line (production host): expi293 / Production host: Homo sapiens (human) / References: UniProt: Q15435

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Protein/peptide , 1 types, 1 molecules C

#3: 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.: 1
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, RING-type E3 ubiquitin transferase

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Non-polymers , 3 types, 55 molecules

#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 5.17 Å3/Da / Density % sol: 76.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 1.8 M sodium phosphate monobasic monohydrate, potassium phosphate dibasic pH 8.2

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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: May 20, 2021
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: 27016 / % 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
PHENIX(1.19.1_4122: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→39.46 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2397 2000 7.4 %
Rwork0.2089 --
obs0.2112 27009 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→39.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4822 0 51 44 4917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044941
X-RAY DIFFRACTIONf_angle_d0.9396674
X-RAY DIFFRACTIONf_dihedral_angle_d5.078647
X-RAY DIFFRACTIONf_chiral_restr0.059753
X-RAY DIFFRACTIONf_plane_restr0.005852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.280.35251380.32551723X-RAY DIFFRACTION99
3.28-3.370.33151380.29251730X-RAY DIFFRACTION100
3.37-3.470.29531410.26211755X-RAY DIFFRACTION100
3.47-3.580.27081390.23691752X-RAY DIFFRACTION100
3.58-3.710.27161400.22471749X-RAY DIFFRACTION100
3.71-3.860.25111420.21391764X-RAY DIFFRACTION100
3.86-4.030.22881400.18461770X-RAY DIFFRACTION100
4.03-4.240.18091420.15751765X-RAY DIFFRACTION100
4.25-4.510.16621410.14951769X-RAY DIFFRACTION100
4.51-4.860.19741440.14451797X-RAY DIFFRACTION100
4.86-5.340.18661420.16861781X-RAY DIFFRACTION100
5.34-6.110.21631460.21811821X-RAY DIFFRACTION100
6.12-7.690.31111480.23981854X-RAY DIFFRACTION100
7.7-39.460.2651590.24791979X-RAY DIFFRACTION100

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