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- PDB-5inb: RepoMan-PP1g (protein phosphatase 1, gamma isoform) holoenzyme complex -

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Basic information

Entry
Database: PDB / ID: 5inb
TitleRepoMan-PP1g (protein phosphatase 1, gamma isoform) holoenzyme complex
Components
  • Cell division cycle-associated protein 2
  • Serine/threonine-protein phosphatase PP1-gamma catalytic subunit
KeywordsHYDROLASE/PROTEIN BINDING / PP1 gamma / RepoMan / Ki-67 / Phosphatase / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


PTW/PP1 phosphatase complex / regulation of nucleocytoplasmic transport / protein phosphatase 1 binding / lamin binding / protein phosphatase regulator activity / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / regulation of mitotic nuclear division / protein serine/threonine phosphatase activity / glycogen metabolic process ...PTW/PP1 phosphatase complex / regulation of nucleocytoplasmic transport / protein phosphatase 1 binding / lamin binding / protein phosphatase regulator activity / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / regulation of mitotic nuclear division / 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 / microtubule organizing center / cleavage furrow / mitotic sister chromatid segregation / phosphoprotein phosphatase activity / blastocyst development / protein dephosphorylation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / positive regulation of glial cell proliferation / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / Downregulation of TGF-beta receptor signaling / chromosome segregation / RHO GTPases Activate Formins / RAF activation / circadian regulation of gene expression / regulation of circadian rhythm / kinetochore / neuron differentiation / Separation of Sister Chromatids / : / MAPK cascade / presynapse / chromosome / midbody / spermatogenesis / dendritic spine / mitochondrial outer membrane / nuclear speck / protein domain specific binding / cell division / focal adhesion / protein-containing complex binding / protein kinase binding / nucleolus / glutamatergic synapse / protein-containing complex / mitochondrion / RNA binding / nucleoplasm / metal ion binding / nucleus / 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
MALONATE ION / Serine/threonine-protein phosphatase PP1-gamma catalytic subunit / Cell division cycle-associated protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 7, 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-gamma catalytic subunit
B: Cell division cycle-associated protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,81610
Polymers40,1382
Non-polymers6788
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-18 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.371, 86.371, 215.894
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Serine/threonine-protein phosphatase PP1-gamma catalytic subunit / PP-1G / Protein phosphatase 1C catalytic subunit


Mass: 35044.363 Da / Num. of mol.: 1 / Fragment: UNP residues 7-308
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CC / Plasmid: RP1B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P36873, protein-serine/threonine phosphatase
#2: Protein/peptide Cell division cycle-associated protein 2 / Recruits PP1 onto mitotic chromatin at anaphase protein / Repo-Man


Mass: 5093.903 Da / Num. of mol.: 1 / Fragment: PP1 binding domain (UNP residues 383-423)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDCA2 / Plasmid: petM30-MBP / Production host: Escherichia coli (E. coli) / References: UniProt: Q69YH5

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Non-polymers , 4 types, 312 molecules

#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.9 Å3/Da / Density % sol: 57.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.3 / Details: 1 M Sodium Malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 14, 2015
RadiationMonochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→37.4 Å / Num. obs: 234338 / % possible obs: 100 % / Observed criterion σ(I): 2.4 / Redundancy: 8.9 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 23.5
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.0927 / Mean I/σ(I) obs: 2.4 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSNov 3, 2014data reduction
AimlessNov 3, 2014data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JK7

1jk7


Resolution: 1.3→37.4 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 13.01
RfactorNum. reflection% reflection
Rfree0.1534 10829 4.89 %
Rwork0.1324 --
obs0.1334 221393 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.3→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2591 0 44 304 2939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082905
X-RAY DIFFRACTIONf_angle_d1.2433962
X-RAY DIFFRACTIONf_dihedral_angle_d12.8241134
X-RAY DIFFRACTIONf_chiral_restr0.089425
X-RAY DIFFRACTIONf_plane_restr0.005526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3003-1.31510.26413470.24066970X-RAY DIFFRACTION99
1.3151-1.33060.23443550.21667071X-RAY DIFFRACTION100
1.3306-1.34680.22943250.20967036X-RAY DIFFRACTION100
1.3468-1.36380.21793540.19766967X-RAY DIFFRACTION100
1.3638-1.38180.22633880.18787024X-RAY DIFFRACTION100
1.3818-1.40070.18093740.17196985X-RAY DIFFRACTION100
1.4007-1.42070.18433690.16427046X-RAY DIFFRACTION100
1.4207-1.44190.19324070.15987019X-RAY DIFFRACTION100
1.4419-1.46450.18233570.14977012X-RAY DIFFRACTION100
1.4645-1.48850.18683700.14047003X-RAY DIFFRACTION100
1.4885-1.51410.17063650.12986999X-RAY DIFFRACTION100
1.5141-1.54170.14613960.12467022X-RAY DIFFRACTION100
1.5417-1.57130.15593420.11747060X-RAY DIFFRACTION100
1.5713-1.60340.13593360.10816984X-RAY DIFFRACTION100
1.6034-1.63830.15363370.10937035X-RAY DIFFRACTION100
1.6383-1.67640.13353520.10347036X-RAY DIFFRACTION100
1.6764-1.71830.13393900.10347008X-RAY DIFFRACTION100
1.7183-1.76480.12983870.10347003X-RAY DIFFRACTION100
1.7648-1.81670.12223810.10456987X-RAY DIFFRACTION100
1.8167-1.87530.14534070.10097024X-RAY DIFFRACTION100
1.8753-1.94240.12343810.10686934X-RAY DIFFRACTION100
1.9424-2.02010.13013480.11027075X-RAY DIFFRACTION100
2.0201-2.1120.13383940.11236979X-RAY DIFFRACTION100
2.112-2.22340.14393550.11337006X-RAY DIFFRACTION100
2.2234-2.36270.1573740.12296996X-RAY DIFFRACTION100
2.3627-2.54510.1453170.13087094X-RAY DIFFRACTION100
2.5451-2.80110.14392930.13247068X-RAY DIFFRACTION100
2.8011-3.20620.15543350.14197040X-RAY DIFFRACTION100
3.2062-4.03880.1523250.13847074X-RAY DIFFRACTION100
4.0388-37.41520.16033680.15117007X-RAY DIFFRACTION100

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