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Yorodumi- PDB-6c83: Structure of Aurora A (122-403) bound to inhibitory Monobody Mb2 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6c83 | ||||||||||||
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Title | Structure of Aurora A (122-403) bound to inhibitory Monobody Mb2 and AMPPCP | ||||||||||||
Components |
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Keywords | transferase/inhibitor / Transferase / Aurora A / Monobody / AMPPCP / Kinase / Activation / Allostery / Cell cycle / Cancer / transferase-inhibitor complex | ||||||||||||
Function / homology | Function and homology information Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / 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 ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / 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 / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / 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 / 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 / basolateral plasma membrane / peptidyl-serine phosphorylation / proteasome-mediated ubiquitin-dependent protein catabolic process / Regulation of TP53 Activity through Phosphorylation / protein autophosphorylation / 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) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||||||||
Authors | Hoemberger, M. / Kutter, S. / Zorba, A. / Nguyen, V. / Shohei, A. / Shohei, K. / Kern, D. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: Allosteric modulation of a human protein kinase with monobodies. Authors: Zorba, A. / Nguyen, V. / Koide, A. / Hoemberger, M. / Zheng, Y. / Kutter, S. / Kim, C. / Koide, S. / Kern, D. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6c83.cif.gz | 302.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c83.ent.gz | 211 KB | Display | PDB format |
PDBx/mmJSON format | 6c83.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6c83_validation.pdf.gz | 976.6 KB | Display | wwPDB validaton report |
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Full document | 6c83_full_validation.pdf.gz | 987.2 KB | Display | |
Data in XML | 6c83_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 6c83_validation.cif.gz | 31.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/6c83 ftp://data.pdbj.org/pub/pdb/validation_reports/c8/6c83 | HTTPS FTP |
-Related structure data
Related structure data | 5g15C 3k2mS 4c3rS 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
#1: Protein | Mass: 32990.754 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: AURKA, AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, STK15, STK6 Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O14965, non-specific serine/threonine protein kinase #2: Protein | Mass: 9853.987 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) #3: Chemical | |
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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: 2.23 Å3/Da / Density % sol: 44.94 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Crystals of dephosphorylated Aurora A (122-403) in complex with Monobody Mb2 and AMPPCP were obtained by mixing a 1:1 ratio of 0.24mM Aurora A, 0.25mM Mb2 and 2.5mM AMPPCP in 20mM TrisHCl pH ...Details: Crystals of dephosphorylated Aurora A (122-403) in complex with Monobody Mb2 and AMPPCP were obtained by mixing a 1:1 ratio of 0.24mM Aurora A, 0.25mM Mb2 and 2.5mM AMPPCP in 20mM TrisHCl pH 7.5, 200mM NaCl,20mM MgCl2, 10% glycerol, 5mM TCEP with mother liquor (0.1M Bis-Tris pH 5.5, 0.2M NaCl, 25% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2017 |
Radiation | Monochromator: Si(111) side scattering I-beam bent single crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→64.86 Å / Num. obs: 25451 / % possible obs: 98.47 % / Redundancy: 5.3 % / Biso Wilson estimate: 62.83 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.55→2.62 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4c3r, 3k2m Resolution: 2.55→46.82 Å / SU ML: 0.4642 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.2497
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→46.82 Å
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Refine LS restraints |
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LS refinement shell |
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