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- PDB-5j28: Ki67-PP1g (protein phosphatase 1, gamma isoform) holoenzyme complex -

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Basic information

Entry
Database: PDB / ID: 5j28
TitleKi67-PP1g (protein phosphatase 1, gamma isoform) holoenzyme complex
Components
  • Antigen KI-67
  • 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


regulation of chromosome segregation / PTW/PP1 phosphatase complex / regulation of nucleocytoplasmic transport / regulation of chromatin organization / protein phosphatase 1 binding / lamin binding / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / microtubule organizing center / regulation of mitotic nuclear division ...regulation of chromosome segregation / PTW/PP1 phosphatase complex / regulation of nucleocytoplasmic transport / regulation of chromatin organization / protein phosphatase 1 binding / lamin binding / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / microtubule organizing center / regulation of mitotic nuclear division / myosin phosphatase activity / protein serine/threonine phosphatase activity / glycogen metabolic process / protein-serine/threonine phosphatase / entrainment of circadian clock by photoperiod / Triglyceride catabolism / phosphatase activity / phosphoprotein phosphatase activity / cleavage furrow / blastocyst development / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / positive regulation of glial cell proliferation / Resolution of Sister Chromatid Cohesion / Downregulation of TGF-beta receptor signaling / protein dephosphorylation / RHO GTPases Activate Formins / RAF activation / circadian regulation of gene expression / regulation of circadian rhythm / neuron differentiation / kinetochore / Separation of Sister Chromatids / MAPK cascade / Circadian Clock / presynapse / chromosome / midbody / spermatogenesis / cell population proliferation / mitochondrial outer membrane / dendritic spine / nuclear body / nuclear speck / cell cycle / cell division / protein domain specific binding / focal adhesion / glutamatergic synapse / protein-containing complex binding / nucleolus / protein kinase binding / protein-containing complex / mitochondrion / DNA binding / RNA binding / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
KI67R / KI67R (NUC007) repeat / K167/Chmadrin repeat / 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 ...KI67R / KI67R (NUC007) repeat / K167/Chmadrin repeat / 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 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / SMAD/FHA domain superfamily / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / Serine/threonine-protein phosphatase PP1-gamma catalytic subunit / Proliferation marker protein Ki-67
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 29, 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

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase PP1-gamma catalytic subunit
B: Serine/threonine-protein phosphatase PP1-gamma catalytic subunit
C: Antigen KI-67
D: Antigen KI-67
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6907
Polymers80,4634
Non-polymers2273
Water4,179232
1
A: Serine/threonine-protein phosphatase PP1-gamma catalytic subunit
C: Antigen KI-67
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3564
Polymers40,2312
Non-polymers1252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-25 kcal/mol
Surface area13420 Å2
MethodPISA
2
B: Serine/threonine-protein phosphatase PP1-gamma catalytic subunit
D: Antigen KI-67
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3333
Polymers40,2312
Non-polymers1021
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-13 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.832, 90.832, 206.717
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 35044.363 Da / Num. of mol.: 2 / 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)
References: UniProt: P36873, protein-serine/threonine phosphatase
#2: Protein/peptide Antigen KI-67


Mass: 5187.017 Da / Num. of mol.: 2 / Fragment: UNP residues 496-536 / Mutation: T525M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MKI67 / Plasmid: pet-M30 MBP / Production host: Escherichia coli (E. coli) / References: UniProt: P46013
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 232 / 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: 3.06 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 1.9 M Sodium Malonate pH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2016
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: 2→39.331 Å / Num. obs: 64993 / % possible obs: 100 % / Observed criterion σ(I): 3.1 / Redundancy: 10.4 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 20.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.0861 / Mean I/σ(I) obs: 3.1 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSNov 3, 2014data reduction
AimlessNov 3, 2014data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5INB

5inb


Resolution: 2→39.331 Å / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.23 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1972 1998 3.08 %
Rwork0.1538 --
obs0.1593 64920 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→39.331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5134 0 15 232 5381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075283
X-RAY DIFFRACTIONf_angle_d0.8617156
X-RAY DIFFRACTIONf_dihedral_angle_d11.7323160
X-RAY DIFFRACTIONf_chiral_restr0.047770
X-RAY DIFFRACTIONf_plane_restr0.005946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0002-2.05020.27971420.21594470X-RAY DIFFRACTION97
2.0502-2.10570.25331410.20774500X-RAY DIFFRACTION97
2.1057-2.16760.23121420.20134501X-RAY DIFFRACTION97
2.1676-2.23760.23321440.19874465X-RAY DIFFRACTION97
2.2376-2.31750.24121410.1994479X-RAY DIFFRACTION97
2.3175-2.41030.24611430.18194464X-RAY DIFFRACTION97
2.4103-2.520.18321440.17254510X-RAY DIFFRACTION97
2.52-2.65280.22561460.17334481X-RAY DIFFRACTION97
2.6528-2.8190.21571450.17064495X-RAY DIFFRACTION97
2.819-3.03660.19571420.15684490X-RAY DIFFRACTION97
3.0366-3.3420.21851420.16314490X-RAY DIFFRACTION97
3.342-3.82520.18391380.14494505X-RAY DIFFRACTION97
3.8252-4.81790.11991430.12094504X-RAY DIFFRACTION97
4.8179-38.64540.20181450.13864534X-RAY DIFFRACTION97

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