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Yorodumi- PDB-5g15: Structure Aurora A (122-403) bound to activating monobody Mb1 and... -
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-Basic information
Entry | Database: PDB / ID: 5g15 | ||||||
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Title | Structure Aurora A (122-403) bound to activating monobody Mb1 and AMPPCP | ||||||
Components |
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Keywords | TRANSFERASE / AURORA A / MONOBODY / AMPPCP / KINASE / ACTIVATION / ALLOSTERY / CELL CYCLE / CANCER | ||||||
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: 2.06 Å | ||||||
Authors | Zorba, A. / Kutter, S. / Kern, D. / Koide, S. / Koide, A. | ||||||
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 | 5g15.cif.gz | 92.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g15.ent.gz | 69.4 KB | Display | PDB format |
PDBx/mmJSON format | 5g15.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g15_validation.pdf.gz | 767.3 KB | Display | wwPDB validaton report |
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Full document | 5g15_full_validation.pdf.gz | 769.6 KB | Display | |
Data in XML | 5g15_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 5g15_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/5g15 ftp://data.pdbj.org/pub/pdb/validation_reports/g1/5g15 | HTTPS FTP |
-Related structure data
Related structure data | 6c83C 3k2mS 4c3rS 5g16 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 on special symmetry positions |
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-Components
-Protein / Antibody , 2 types, 2 molecules AB
#1: Protein | Mass: 32689.459 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, UNP RESIDUES 122-403 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) References: UniProt: O14965, non-specific serine/threonine protein kinase |
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#2: Antibody | Mass: 10577.592 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PET28A / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) |
-Non-polymers , 4 types, 151 molecules
#3: Chemical | ChemComp-ACP / | ||
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#4: Chemical | ChemComp-MG / | ||
#5: Chemical | ChemComp-SO4 / #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: 2.86 Å3/Da / Density % sol: 57.04 % / Description: NONE |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: AURORA A AND MONOBODIES WERE ALIQUOTED IN STORAGE BUFFER (20MM TRISHCL, 200MM NACL, 10% (V/V) GLYCEROL, 20MM MGCL2, 5MM TCEP, PH 7.50) AND KEPT AT -80C. AMPPCP WAS PREPARED FRESH FROM POWDER ...Details: AURORA A AND MONOBODIES WERE ALIQUOTED IN STORAGE BUFFER (20MM TRISHCL, 200MM NACL, 10% (V/V) GLYCEROL, 20MM MGCL2, 5MM TCEP, PH 7.50) AND KEPT AT -80C. AMPPCP WAS PREPARED FRESH FROM POWDER THE DAY OF CRYSTALLIZATION IN CONCENTRATIONS OF 100-120MM IN STORAGE BUFFER. CRYSTALS OF AURA IN COMPLEX WITH AMPPCP AND ACTIVATING MONOBODY, MB1, WERE OBTAINED BY COMBINING 0.5UL OF [300UM AURA WITH 5MM AMPPCP AND 300UM MB1] WITH 0.5UL OF MOTHER LIQUOR (0.1M MES SODIUM SALT PH 6.50, 0.2M AMMONIUM SULFATE, 4% (V/V) 1,3-PROPANEDIOL, 30% (W/V) PEG8000). CRYSTALS WERE GROWN AT 18C BY VAPOR DIFFUSION AND THE SITTING DROP METHOD. THE CRYSTALS WERE WASHED WITH MOTHER LIQUOR AND FLASH FROZEN IN LIQUID NITROGEN IN PREPARATION FOR DATA COLLECTION. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99992 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 9, 2015 |
Radiation | Monochromator: DOUBLE-CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99992 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→58.13 Å / Num. obs: 30879 / % possible obs: 100 % / Observed criterion σ(I): 1.8 / Redundancy: 7.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.06→2.12 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 1.8 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 4C3R AND 3K2M Resolution: 2.06→77.1 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.946 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.133 Å2
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Refinement step | Cycle: LAST / Resolution: 2.06→77.1 Å
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Refine LS restraints |
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