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Yorodumi- PDB-5inb: RepoMan-PP1g (protein phosphatase 1, gamma isoform) holoenzyme complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 5inb | |||||||||
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Title | RepoMan-PP1g (protein phosphatase 1, gamma isoform) holoenzyme complex | |||||||||
Components |
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Keywords | HYDROLASE/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 / 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 ...regulation of chromosome segregation / PTW/PP1 phosphatase complex / regulation of nucleocytoplasmic transport / 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 / positive regulation of protein dephosphorylation / Resolution of Sister Chromatid Cohesion / Downregulation of TGF-beta receptor signaling / protein dephosphorylation / chromosome segregation / 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 / mitochondrial outer membrane / dendritic spine / 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 / RNA binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | |||||||||
Authors | Kumar, G.S. / Peti, W. / Page, R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5inb.cif.gz | 162.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5inb.ent.gz | 126.7 KB | Display | PDB format |
PDBx/mmJSON format | 5inb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/5inb ftp://data.pdbj.org/pub/pdb/validation_reports/in/5inb | HTTPS FTP |
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-Related structure data
Related structure data | 5iohC 5j28C 1jk7S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | 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 |
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#2: Protein/peptide | 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 |
-Non-polymers , 4 types, 312 molecules
#3: Chemical | ChemComp-MLI / | ||||
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#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.52 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.3 / Details: 1 M Sodium Malonate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 14, 2015 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 1.3→1.32 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.0927 / Mean I/σ(I) obs: 2.4 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JK7 Resolution: 1.3→37.4 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 13.01
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→37.4 Å
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Refine LS restraints |
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LS refinement shell |
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