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- PDB-5ioh: RepoMan-PP1a (protein phosphatase 1, alpha isoform) holoenzyme complex -

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Basic information

Entry
Database: PDB / ID: 5ioh
TitleRepoMan-PP1a (protein phosphatase 1, alpha isoform) holoenzyme complex
Components
  • Cell division cycle-associated protein 2
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE/PROTEIN BINDING / PP1 alpha / RepoMan / Ki-67 / Phosphatase / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


regulation of glycogen catabolic process / regulation of chromosome segregation / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / 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 / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand ...regulation of glycogen catabolic process / regulation of chromosome segregation / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / 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 / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / regulation of canonical Wnt signaling pathway / regulation of mitotic nuclear division / dephosphorylation / branching morphogenesis of an epithelial tube / protein serine/threonine phosphatase activity / glycogen metabolic process / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / Triglyceride catabolism / entrainment of circadian clock by photoperiod / Maturation of hRSV A proteins / phosphatase activity / telomere maintenance in response to DNA damage / phosphoprotein phosphatase activity / transition metal ion binding / DARPP-32 events / positive regulation of glycogen biosynthetic process / ribonucleoprotein complex binding / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / adherens junction / chromosome segregation / lung development / circadian regulation of gene expression / response to lead ion / regulation of circadian rhythm / : / presynapse / chromosome / perikaryon / dendritic spine / iron ion binding / cell division / nucleolus / glutamatergic synapse / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Protein phosphatase 1 binding domain / Protein phosphatase 1 binding / 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 ...Protein phosphatase 1 binding domain / Protein phosphatase 1 binding / 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
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / Cell division cycle-associated protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.566 Å
AuthorsKumar, G.S. / Peti, W. / Page, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098482 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1R01NS091336 United States
CitationJournal: Elife / Year: 2016
Title: The Ki-67 and RepoMan mitotic phosphatases assemble via an identical, yet novel mechanism.
Authors: Kumar, G.S. / Gokhan, E. / De Munter, S. / Bollen, M. / Vagnarelli, P. / Peti, W. / Page, R.
History
DepositionMar 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Cell division cycle-associated protein 2
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: Cell division cycle-associated protein 2


Theoretical massNumber of molelcules
Total (without water)82,3704
Polymers82,3704
Non-polymers00
Water2,738152
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
B: Cell division cycle-associated protein 2


Theoretical massNumber of molelcules
Total (without water)41,1852
Polymers41,1852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-16 kcal/mol
Surface area12700 Å2
MethodPISA
2
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: Cell division cycle-associated protein 2


Theoretical massNumber of molelcules
Total (without water)41,1852
Polymers41,1852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-14 kcal/mol
Surface area13170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.769, 57.089, 73.635
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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 / Plasmid: RP1B / Production host: Escherichia coli (E. coli)
References: UniProt: P62136, protein-serine/threonine phosphatase
#2: Protein Cell division cycle-associated protein 2 / Recruits PP1 onto mitotic chromatin at anaphase protein / Repo-Man


Mass: 7023.053 Da / Num. of mol.: 2 / Fragment: UNP residues 383-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDCA2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q69YH5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.05 Å3/Da / Density % sol: 40.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 100 mM Sodium Malonate, 12% PEG 3350

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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: Nov 12, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.566→50 Å / Num. obs: 22441 / % possible obs: 99.3 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.017 / Net I/σ(I): 15.3
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2.4 / % possible all: 90.4

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MOV

4mov


Resolution: 2.566→46.545 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2152 1118 5.07 %
Rwork0.1764 --
obs0.1785 22041 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.566→46.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5071 0 0 152 5223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025186
X-RAY DIFFRACTIONf_angle_d0.617036
X-RAY DIFFRACTIONf_dihedral_angle_d10.5161881
X-RAY DIFFRACTIONf_chiral_restr0.024772
X-RAY DIFFRACTIONf_plane_restr0.002924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5662-2.68290.27971050.22912273X-RAY DIFFRACTION87
2.6829-2.82440.27551510.21422622X-RAY DIFFRACTION100
2.8244-3.00130.27121420.20242619X-RAY DIFFRACTION100
3.0013-3.2330.21381420.19762604X-RAY DIFFRACTION100
3.233-3.55820.27031520.18142626X-RAY DIFFRACTION100
3.5582-4.07290.19411390.16432667X-RAY DIFFRACTION100
4.0729-5.13030.15371400.13772689X-RAY DIFFRACTION100
5.1303-46.55270.19931470.17182823X-RAY DIFFRACTION100

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