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- PDB-4moy: Structure of a second nuclear PP1 Holoenzyme, crystal form 1 -

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Basic information

Entry
Database: PDB / ID: 4moy
TitleStructure of a second nuclear PP1 Holoenzyme, crystal form 1
Components(Serine/threonine-protein phosphatase ...) x 2
KeywordsHYDROLASE/NUCLEAR PROTEIN / Serine/threonine phosphatase / Nucleus / HYDROLASE-NUCLEAR PROTEIN complex
Function / homology
Function and homology information


negative regulation of mitotic DNA damage checkpoint / 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 / glycogen granule / regulation of translational initiation in response to stress / RNA polymerase II promoter clearance / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / cadherin binding involved in cell-cell adhesion ...negative regulation of mitotic DNA damage checkpoint / 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 / glycogen granule / regulation of translational initiation in response to stress / 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 / protein phosphatase regulator activity / regulation of canonical Wnt signaling pathway / glycogen metabolic process / protein dephosphorylation / Phosphorylation and nuclear translocation of the CRY:PER:kinase complex / protein phosphatase inhibitor activity / Triglyceride catabolism / protein-serine/threonine phosphatase / entrainment of circadian clock by photoperiod / negative regulation of transcription elongation by RNA polymerase II / telomere maintenance in response to DNA damage / phosphatase activity / protein serine/threonine phosphatase activity / Maturation of hRSV A proteins / positive regulation of telomere maintenance / negative regulation of cardiac muscle cell apoptotic process / transition metal ion binding / positive regulation of glycogen biosynthetic process / DARPP-32 events / enzyme-substrate adaptor activity / ribonucleoprotein complex binding / positive regulation of Ras protein signal transduction / phosphoprotein phosphatase activity / Downregulation of TGF-beta receptor signaling / circadian regulation of gene expression / adherens junction / positive regulation of transcription elongation by RNA polymerase II / response to lead ion / regulation of circadian rhythm / mRNA Polyadenylation / presynapse / dendritic spine / perikaryon / nuclear body / chromosome, telomeric region / protein stabilization / iron ion binding / cell division / nucleolus / chromatin / glutamatergic synapse / endoplasmic reticulum / DNA binding / RNA binding / extracellular exosome / nucleoplasm / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Serine-threonine protein phosphatase, N-terminal / Serine-threonine protein phosphatase N-terminal domain / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / TFIIS N-terminal domain profile. / TFIIS helical bundle-like domain / Transcription factor IIS, N-terminal / Zinc finger, CCCH-type superfamily ...: / Serine-threonine protein phosphatase, N-terminal / Serine-threonine protein phosphatase N-terminal domain / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / TFIIS N-terminal domain profile. / TFIIS helical bundle-like domain / Transcription factor IIS, N-terminal / Zinc finger, CCCH-type superfamily / zinc finger / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Metallo-dependent phosphatases / TFIIS/LEDGF domain superfamily / 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
: / PHOSPHATE ION / Serine/threonine-protein phosphatase 1 regulatory subunit 10 / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1953 Å
AuthorsChoy, M.S. / Hieke, M. / Peti, W. / Page, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Understanding the antagonism of retinoblastoma protein dephosphorylation by PNUTS provides insights into the PP1 regulatory code.
Authors: Choy, M.S. / Hieke, M. / Kumar, G.S. / Lewis, G.R. / Gonzalez-Dewhitt, K.R. / Kessler, R.P. / Stein, B.J. / Hessenberger, M. / Nairn, A.C. / Peti, W. / Page, R.
History
DepositionSep 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 1 regulatory subunit 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8068
Polymers39,3812
Non-polymers4246
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-46 kcal/mol
Surface area13370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.788, 130.788, 47.725
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-530-

HOH

21A-566-

HOH

31A-624-

HOH

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Components

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Serine/threonine-protein phosphatase ... , 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 / Fragment: PP1 alpha catalytic subunit
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 Serine/threonine-protein phosphatase 1 regulatory subunit 10 / MHC class I region proline-rich protein CAT53 / Phosphatase 1 nuclear targeting subunit / Protein PNUTS


Mass: 5218.873 Da / Num. of mol.: 1 / Fragment: PP1 Nuclear Targeting Subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ppp1r10, Cat53, Pnuts / Production host: Escherichia coli (E. coli) / References: UniProt: O55000

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Non-polymers , 5 types, 165 molecules

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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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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: 2.99 Å3/Da / Density % sol: 58.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.1 M Tris, 1 M LiCl, 18% PEG 6000, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.195→43.98 Å / Num. all: 24218 / Num. obs: 24217 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3
Reflection shellResolution: 2.195→2.24 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1953→43.98 Å / SU ML: 0.22 / σ(F): 1.37 / Phase error: 19.05 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1852 1237 5.11 %Random
Rwork0.1514 ---
all0.1531 24221 --
obs0.1531 24199 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1953→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2585 0 20 159 2764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012686
X-RAY DIFFRACTIONf_angle_d1.1843656
X-RAY DIFFRACTIONf_dihedral_angle_d13.056971
X-RAY DIFFRACTIONf_chiral_restr0.077393
X-RAY DIFFRACTIONf_plane_restr0.005472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1953-2.28310.25721370.21192534X-RAY DIFFRACTION99
2.2831-2.3870.23221340.18072525X-RAY DIFFRACTION100
2.387-2.51290.23271350.17412527X-RAY DIFFRACTION100
2.5129-2.67030.22251420.17222516X-RAY DIFFRACTION100
2.6703-2.87640.24971290.17522526X-RAY DIFFRACTION100
2.8764-3.16580.22051430.16622564X-RAY DIFFRACTION100
3.1658-3.62380.20321490.15512538X-RAY DIFFRACTION100
3.6238-4.56480.151380.11792557X-RAY DIFFRACTION100
4.5648-43.98910.14031300.14532675X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.04670.19460.28514.05261.33021.84670.0293-0.0347-0.06760.137-0.30880.64970.0728-0.22750.24010.17950.01870.04020.2179-0.0640.234842.368222.670419.4766
20.5233-0.34780.4311.37160.26822.156-0.01230.2832-0.1040.0927-0.25770.0916-0.0042-0.49730.10670.2648-0.0420.01990.3914-0.03040.239255.086928.940520.7716
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 300 )
2X-RAY DIFFRACTION2chain 'B' and (resid 390 through 424 )

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