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Open data
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Basic information
Entry | Database: PDB / ID: 4mjs | ||||||
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Title | crystal structure of a PB1 complex | ||||||
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![]() | TRANSFERASE/PROTEIN BINDING / PB1 domain / PB1 heterodimer and protein interaction / TRANSFERASE-PROTEIN BINDING complex | ||||||
Function / homology | ![]() TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / VEGFR2 mediated cell proliferation / calcium,diacylglycerol-dependent serine/threonine kinase activity / activation of phospholipase D activity / protein localization => GO:0008104 / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / protein kinase C signaling / negative regulation of peptidyl-tyrosine phosphorylation / regulation of Ras protein signal transduction ...TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / VEGFR2 mediated cell proliferation / calcium,diacylglycerol-dependent serine/threonine kinase activity / activation of phospholipase D activity / protein localization => GO:0008104 / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / protein kinase C signaling / negative regulation of peptidyl-tyrosine phosphorylation / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / Estrogen-stimulated signaling through PRKCZ / Lewy body / RHO GTPases Activate NADPH Oxidases / protein kinase C / response to mitochondrial depolarisation / aggrephagy / amphisome / negative regulation of toll-like receptor 4 signaling pathway / positive regulation of T-helper 2 cell differentiation / diacylglycerol-dependent serine/threonine kinase activity / myelin sheath abaxonal region / positive regulation of T-helper 2 cell cytokine production / positive regulation of protein transport / vesicle transport along microtubule / pexophagy / apical cortex / regulation of protein complex stability / autophagy of mitochondrion / endosome organization / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / molecular sequestering activity / non-membrane-bounded organelle assembly / axon hillock / membrane hyperpolarization / negative regulation of hydrolase activity / phagophore assembly site / regulation of mitochondrion organization / aggresome / regulation of canonical NF-kappaB signal transduction / Nuclear events mediated by NFE2L2 / ubiquitin-modified protein reader activity / autolysosome / positive regulation of cell-matrix adhesion / microtubule organizing center / K63-linked polyubiquitin modification-dependent protein binding / intracellular non-membrane-bounded organelle / neuron projection extension / endosomal transport / temperature homeostasis / immune system process / establishment of cell polarity / positive regulation of interleukin-4 production / cell leading edge / membrane depolarization / positive regulation of excitatory postsynaptic potential / positive regulation of interleukin-10 production / phospholipase binding / mitophagy / potassium channel regulator activity / autophagosome / bicellular tight junction / positive regulation of synaptic transmission / negative regulation of protein-containing complex assembly / long-term memory / positive regulation of autophagy / signaling adaptor activity / energy homeostasis / positive regulation of insulin receptor signaling pathway / stress fiber / inclusion body / negative regulation of protein ubiquitination / sperm midpiece / 14-3-3 protein binding / protein sequestering activity / p75NTR recruits signalling complexes / PINK1-PRKN Mediated Mitophagy / Pexophagy / negative regulation of insulin receptor signaling pathway / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / activation of protein kinase B activity / sarcomere / SH2 domain binding / molecular condensate scaffold activity / ubiquitin binding / positive regulation of long-term synaptic potentiation / protein localization to plasma membrane / response to ischemia / long-term synaptic potentiation / protein kinase C binding / macroautophagy / positive regulation of protein localization to plasma membrane / ionotropic glutamate receptor binding / P-body / protein catabolic process / protein localization / receptor tyrosine kinase binding / PML body Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ren, J. / Wang, Z.X. / Wu, J.W. | ||||||
![]() | ![]() Title: Structural and biochemical insights into the homotypic PB1-PB1 complex between PKC zeta and p62 Authors: Ren, J. / Wang, J. / Wang, Z.X. / Wu, J.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 414.5 KB | Display | ![]() |
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PDB format | ![]() | 341.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 634.5 KB | Display | ![]() |
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Full document | ![]() | 676.2 KB | Display | |
Data in XML | ![]() | 74.8 KB | Display | |
Data in CIF | ![]() | 102.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1wmhS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
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Components
#1: Protein | Mass: 10287.679 Da / Num. of mol.: 12 / Fragment: PB1 domain, UNP residues 15-101 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 11542.182 Da / Num. of mol.: 12 / Fragment: PB1 domain, UNP residues 3-102 / Mutation: D69A,D71R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.3 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris-HCl, 8% PEG8000, 0.4M MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 22, 2011 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97892 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. all: 105540 / Num. obs: 105401 / % possible obs: 100 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 7.3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 4.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1WMH Resolution: 2.5→39.534 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 29.45 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.28 Å2 / ksol: 0.31 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5→39.534 Å
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Refine LS restraints |
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LS refinement shell |
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