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Yorodumi- PDB-6vpg: TPX2 residues 7-20 fused to Aurora A residues 116-389 in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vpg | |||||||||||||||
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Title | TPX2 residues 7-20 fused to Aurora A residues 116-389 in complex with AMP-PNP | |||||||||||||||
Components | TPX2 fragment - Aurora A kinase domain fusion | |||||||||||||||
Keywords | TRANSFERASE / Ser/Thr kinase | |||||||||||||||
Function / homology | Function and homology information nuclear microtubule / microtubule nucleation / Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / importin-alpha family protein binding / negative regulation of microtubule depolymerization / spindle assembly involved in female meiosis I / cilium disassembly / positive regulation of oocyte maturation ...nuclear microtubule / microtubule nucleation / Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / importin-alpha family protein binding / negative regulation of microtubule depolymerization / spindle assembly involved in female meiosis I / cilium disassembly / positive regulation of oocyte maturation / spindle pole centrosome / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / meiotic spindle / mitotic centrosome separation / germinal vesicle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / neuron projection extension / spindle organization / positive regulation of mitochondrial fission / intercellular bridge / activation of protein kinase activity / protein kinase activator activity / mitotic spindle pole / SUMOylation of DNA replication proteins / mitotic spindle assembly / spindle midzone / regulation of mitotic spindle organization / regulation of G2/M transition of mitotic cell cycle / centriole / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic cell cycle / positive regulation of mitotic nuclear division / AURKA Activation by TPX2 / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / mitotic spindle organization / ciliary basal body / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / negative regulation of protein binding / molecular function activator activity / liver regeneration / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / regulation of protein stability / spindle microtubule / mitotic spindle / kinetochore / spindle pole / response to wounding / spindle / G2/M transition of mitotic cell cycle / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / microtubule binding / basolateral plasma membrane / peptidyl-serine phosphorylation / proteasome-mediated ubiquitin-dependent protein catabolic process / Regulation of TP53 Activity through Phosphorylation / protein autophosphorylation / molecular adaptor activity / postsynaptic density / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / cell division / protein phosphorylation / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.64 Å | |||||||||||||||
Authors | Lim, D.C. / Yaffe, M.B. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Sci.Signal. / Year: 2020 Title: Redox priming promotes Aurora A activation during mitosis. Authors: Lim, D.C. / Joukov, V. / Rettenmaier, T.J. / Kumagai, A. / Dunphy, W.G. / Wells, J.A. / Yaffe, M.B. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vpg.cif.gz | 139.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vpg.ent.gz | 107 KB | Display | PDB format |
PDBx/mmJSON format | 6vpg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vpg_validation.pdf.gz | 791.7 KB | Display | wwPDB validaton report |
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Full document | 6vpg_full_validation.pdf.gz | 793.1 KB | Display | |
Data in XML | 6vpg_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 6vpg_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/6vpg ftp://data.pdbj.org/pub/pdb/validation_reports/vp/6vpg | HTTPS FTP |
-Related structure data
Related structure data | 6vphC 6vpiC 6vpjC 6vplC 6vpmC 6xkaC 1ol5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34066.715 Da / Num. of mol.: 1 / Fragment: kinase domain,kinase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: TPX2, C20orf1, C20orf2, DIL2, HCA519, AURKA, AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, STK15, STK6 Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 References: UniProt: Q9ULW0, UniProt: O14965, non-specific serine/threonine protein kinase |
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-Non-polymers , 5 types, 68 molecules
#2: Chemical | ChemComp-ANP / | ||||
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#3: Chemical | ChemComp-GOL / | ||||
#4: Chemical | #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.08 % / Mosaicity: 0.705 ° |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 7 Details: 0.1 M HEPES pH 7, 0.9 M KCl, 1.08 M ammonium sulfate, 12% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 12, 2011 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.64→30 Å / Num. obs: 12410 / % possible obs: 99.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.037 / Rrim(I) all: 0.083 / Χ2: 1.057 / Net I/σ(I): 25.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OL5 Resolution: 2.64→27.08 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 215.38 Å2 / Biso min: 42.59 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.64→27.08 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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