[English] 日本語
Yorodumi- PDB-6cpg: Structure of dephosphorylated Aurora A (122-403) in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cpg | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of dephosphorylated Aurora A (122-403) in complex with inhibiting monobody and AT9283 in an inactive conformation | |||||||||||||||
Components |
| |||||||||||||||
Keywords | transferase/inhibitor / protein kinase / DFG-loop / monobody / AT9283 / TRANSFERASE / 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: 2.8 Å | |||||||||||||||
Authors | Otten, R. / Kutter, S. / Zorba, A. / Padua, R.A.P. / Koide, A. / Koide, S. / Kern, D. | |||||||||||||||
Funding support | United States, 4items
| |||||||||||||||
Citation | Journal: Elife / Year: 2018 Title: Dynamics of human protein kinase Aurora A linked to drug selectivity. Authors: Pitsawong, W. / Buosi, V. / Otten, R. / Agafonov, R.V. / Zorba, A. / Kern, N. / Kutter, S. / Kern, G. / Padua, R.A. / Meniche, X. / Kern, D. | |||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6cpg.cif.gz | 303.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6cpg.ent.gz | 199.1 KB | Display | PDB format |
PDBx/mmJSON format | 6cpg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cpg_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6cpg_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6cpg_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 6cpg_validation.cif.gz | 33.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/6cpg ftp://data.pdbj.org/pub/pdb/validation_reports/cp/6cpg | HTTPS FTP |
-Related structure data
Related structure data | 6cpeC 6cpfC 1mq4S 3k2mS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-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 Plasmid: pET28a / Production host: Escherichia coli (E. coli) / 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) / Plasmid: pHBT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) #3: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.05 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: A 1:1 ratio of protein mixture to mother liquor was obtained by combining 0.5 uL of sample [240 uM deP Aurora A + 1.0 mM AT9283 + 250 uM Mb] with 0.5 uL of mother liquor [0.1 M Bis-Tris, pH ...Details: A 1:1 ratio of protein mixture to mother liquor was obtained by combining 0.5 uL of sample [240 uM deP Aurora A + 1.0 mM AT9283 + 250 uM Mb] with 0.5 uL of mother liquor [0.1 M Bis-Tris, pH 5.5, 0.2 M magnesium chloride, 19% (w/v) PEG-3350]. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99997 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2017 |
Radiation | Monochromator: Double-crystal Si(111) and multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99997 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→43.14 Å / Num. obs: 19845 / % possible obs: 99.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 90.44 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.074 / Rrim(I) all: 0.183 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.047 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1418 / CC1/2: 0.625 / Rpim(I) all: 0.559 / Rrim(I) all: 1.338 / % possible all: 98.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MQ4, 3K2M Resolution: 2.8→36.17 Å / SU ML: 0.5484 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.7707
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 85.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→36.17 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|