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- PDB-4mp0: Structure of a second nuclear PP1 Holoenzyme, crystal form 2 -

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Basic information

Entry
Database: PDB / ID: 4mp0
TitleStructure of a second nuclear PP1 Holoenzyme, crystal form 2
Components(Serine/threonine-protein phosphatase ...) x 2
KeywordsHYDROLASE / Serine/threonine phosphatase / Nucleus
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 / 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 ...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 / 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 / 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 cardiac muscle cell apoptotic process / 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 / positive regulation of telomere maintenance / 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 / enzyme-substrate adaptor activity / positive regulation of glycogen biosynthetic process / ribonucleoprotein complex binding / protein dephosphorylation / 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 / : / presynapse / dendritic spine / perikaryon / chromosome, telomeric region / protein stabilization / nuclear body / iron ion binding / cell division / chromatin / nucleolus / glutamatergic synapse / DNA binding / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / nucleus / plasma membrane / 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. / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / 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. / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / 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 / TFIIS/LEDGF domain superfamily / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / 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
: / 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 / MIR / Resolution: 2.1003 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_asym_id / _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_asym_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
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
B: Serine/threonine-protein phosphatase 1 regulatory subunit 10
D: Serine/threonine-protein phosphatase 1 regulatory subunit 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,35612
Polymers78,7624
Non-polymers5948
Water5,675315
1
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)39,7707
Polymers39,3812
Non-polymers3895
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-30 kcal/mol
Surface area13040 Å2
MethodPISA
2
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: Serine/threonine-protein phosphatase 1 regulatory subunit 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5865
Polymers39,3812
Non-polymers2053
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-34 kcal/mol
Surface area12200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.407, 92.407, 199.342
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

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Serine/threonine-protein phosphatase ... , 2 types, 4 molecules ACBD

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


Mass: 34162.148 Da / Num. of mol.: 2 / 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.: 2 / 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 , 4 types, 323 molecules

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


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.7 Å3/Da / Density % sol: 54.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2% v/v Tacsimate, 0.1 M Tris, 16% w/v Polyethylene glycol 3,350, pH 8.5, 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: 2.1→50 Å / Num. all: 51312 / Num. obs: 51308 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3
Reflection shellResolution: 2.1→2.14 Å / % possible all: 99.9

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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: MIR / Resolution: 2.1003→49.836 Å / SU ML: 0.17 / σ(F): 1.37 / Phase error: 19.49 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2017 2578 5.04 %Random
Rwork0.1724 ---
all0.1739 51238 --
obs0.1739 51197 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1003→49.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5040 0 26 315 5381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035233
X-RAY DIFFRACTIONf_angle_d0.8077133
X-RAY DIFFRACTIONf_dihedral_angle_d12.0651874
X-RAY DIFFRACTIONf_chiral_restr0.03775
X-RAY DIFFRACTIONf_plane_restr0.002919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1003-2.14070.26481390.21732642X-RAY DIFFRACTION99
2.1407-2.18440.23361320.19622635X-RAY DIFFRACTION100
2.1844-2.23180.23381380.19042652X-RAY DIFFRACTION100
2.2318-2.28380.23561360.18592676X-RAY DIFFRACTION100
2.2838-2.34090.21961370.17722666X-RAY DIFFRACTION100
2.3409-2.40420.19211440.17332648X-RAY DIFFRACTION100
2.4042-2.47490.20971570.16722660X-RAY DIFFRACTION100
2.4749-2.55480.20131400.17052663X-RAY DIFFRACTION100
2.5548-2.64610.20171590.17212667X-RAY DIFFRACTION100
2.6461-2.7520.19231280.16962685X-RAY DIFFRACTION100
2.752-2.87730.20721350.17832701X-RAY DIFFRACTION100
2.8773-3.02890.22371450.16952682X-RAY DIFFRACTION100
3.0289-3.21870.18591420.18832698X-RAY DIFFRACTION100
3.2187-3.46720.21981450.17322720X-RAY DIFFRACTION100
3.4672-3.8160.20281480.17362716X-RAY DIFFRACTION100
3.816-4.36780.15731530.14712755X-RAY DIFFRACTION100
4.3678-5.50190.181500.15392790X-RAY DIFFRACTION100
5.5019-49.84950.22911500.18832963X-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)
10.97950.083-0.05341.39910.46622.40750.0047-0.0094-0.07640.0264-0.037-0.01170.0622-0.13560.02420.1125-0.0007-0.0150.2417-0.01580.251385.666628.399383.0188
21.1327-0.06050.10970.8089-0.00852.5536-0.0944-0.11890.22950.1659-0.0773-0.0678-1.31040.8582-0.01630.7849-0.2907-0.08660.4118-0.0310.318394.93565.392678.3415
30.3721-0.3411-0.14471.95290.051.496-0.02580.04070.4910.0169-0.05620.0571-0.128-0.51250.0170.191-0.0581-0.05450.4909-0.1180.535172.238723.08377.8746
40.5503-0.0082-0.63010.11950.02790.65930.0382-0.10140.07060.247-0.12870.3335-0.915-0.01770.03261.60160.1051-0.1840.6166-0.21310.924984.173876.161882.8135
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 300 )
2X-RAY DIFFRACTION2chain 'C' and (resid 7 through 297 )
3X-RAY DIFFRACTION3chain 'B' and (resid 396 through 425 )
4X-RAY DIFFRACTION4chain 'D' and (resid 397 through 424 )

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