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- PDB-7t0y: The Ribosomal RNA Processing 1B Protein Phosphatase-1 Holoenzyme -

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Basic information

Entry
Database: PDB / ID: 7t0y
TitleThe Ribosomal RNA Processing 1B Protein Phosphatase-1 Holoenzyme
Components
  • Ribosomal RNA processing protein 1 homolog B
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE / Protein Binding
Function / homology
Function and homology information


granular component / regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation by host of viral transcription / regulation of canonical Wnt signaling pathway ...granular component / regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation by host of viral transcription / regulation of canonical Wnt signaling pathway / regulation of translational initiation / negative regulation of GTPase activity / preribosome, small subunit precursor / myosin phosphatase activity / branching morphogenesis of an epithelial tube / protein serine/threonine phosphatase activity / glycogen metabolic process / protein-serine/threonine phosphatase / Triglyceride catabolism / Maturation of hRSV A proteins / entrainment of circadian clock by photoperiod / phosphatase activity / phosphoprotein phosphatase activity / regulation of RNA splicing / preribosome, large subunit precursor / DARPP-32 events / heterochromatin / ribonucleoprotein complex binding / dephosphorylation / protein dephosphorylation / RNA splicing / Downregulation of TGF-beta receptor signaling / adherens junction / response to lead ion / lung development / circadian regulation of gene expression / euchromatin / regulation of circadian rhythm / mRNA processing / cellular response to virus / rRNA processing / Circadian Clock / presynapse / chromosome / perikaryon / dendritic spine / transcription coactivator activity / positive regulation of apoptotic process / cell cycle / cell division / glutamatergic synapse / apoptotic process / nucleolus / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Ribosomal RNA processing protein 1-like / Nucleolar protein,Nop52 / 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
BROMIDE ION / FLUORIDE ION / : / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / Ribosomal RNA processing protein 1 homolog B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSrivastava, G. / Page, R. / Peti, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM098482 United States
CitationJournal: Cell Rep / Year: 2022
Title: The ribosomal RNA processing 1B:protein phosphatase 1 holoenzyme reveals non-canonical PP1 interaction motifs.
Authors: Srivastava, G. / Bajaj, R. / Kumar, G.S. / Gaudreau-Lapierre, A. / Nicolas, H. / Chamousset, D. / Kreitler, D. / Peti, W. / Trinkle-Mulcahy, L. / Page, R.
History
DepositionNov 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
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

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
B: Ribosomal RNA processing protein 1 homolog B
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: Ribosomal RNA processing protein 1 homolog B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,90223
Polymers78,7414
Non-polymers1,16119
Water8,701483
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
B: Ribosomal RNA processing protein 1 homolog B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,96912
Polymers39,3702
Non-polymers59910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-23 kcal/mol
Surface area14300 Å2
MethodPISA
2
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: Ribosomal RNA processing protein 1 homolog B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,93211
Polymers39,3702
Non-polymers5629
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-26 kcal/mol
Surface area14420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.528, 160.387, 50.615
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11C-554-

HOH

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Components

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

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


Mass: 34191.215 Da / Num. of mol.: 2 / Mutation: Q20R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CA, PPP1A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P62136, protein-serine/threonine phosphatase
#2: Protein/peptide Ribosomal RNA processing protein 1 homolog B / RRP1-like protein B


Mass: 5179.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RRP1B, KIAA0179 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q14684

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Non-polymers , 5 types, 502 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


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


Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F
#6: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% ethylene glycol; 10% PEG8000, 0.1 M imidazole; MES acid, 0.09 M Sodium fluoride; 0.09 M Sodium bromide; 0.09 M Sodium iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→48.27 Å / Num. obs: 61295 / % possible obs: 96.2 % / Redundancy: 4.6 % / Biso Wilson estimate: 26.34 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.207 / Net I/σ(I): 4.9
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.28 / Num. unique obs: 4407 / CC1/2: 0.54 / % possible all: 94.8

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Processing

Software
NameVersionClassification
JBluIce-EPICS1.19.1_4122data collection
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4158phasing
Coot0.9.4.1 ELmodel building
PHENIX1.19.1_4158model building
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MOV

4mov


Resolution: 1.8→48.27 Å / SU ML: 0.3232 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.2841
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2462 1997 3.26 %
Rwork0.2081 59208 -
obs0.2093 61205 95.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.62 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5504 0 52 483 6039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00555709
X-RAY DIFFRACTIONf_angle_d0.81757693
X-RAY DIFFRACTIONf_chiral_restr0.0474824
X-RAY DIFFRACTIONf_plane_restr0.00641005
X-RAY DIFFRACTIONf_dihedral_angle_d13.82742154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.7221390.82394119X-RAY DIFFRACTION94.64
1.85-1.90.3721400.3224160X-RAY DIFFRACTION95.47
1.9-1.950.30161340.24953986X-RAY DIFFRACTION91.27
1.95-2.010.30781380.25164047X-RAY DIFFRACTION93.56
2.01-2.090.3261430.26334249X-RAY DIFFRACTION96.93
2.09-2.170.29671420.23574234X-RAY DIFFRACTION97.05
2.17-2.270.27091430.21764248X-RAY DIFFRACTION97.04
2.27-2.390.28321440.21594267X-RAY DIFFRACTION97.03
2.39-2.540.31131440.21654262X-RAY DIFFRACTION96.84
2.54-2.730.22911410.21264188X-RAY DIFFRACTION95.65
2.73-3.010.24971410.20824160X-RAY DIFFRACTION93.32
3.01-3.440.22621470.19594364X-RAY DIFFRACTION98.39
3.44-4.340.18411500.16164423X-RAY DIFFRACTION98.01
4.34-48.270.18881510.15944501X-RAY DIFFRACTION95.45

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