+Open data
-Basic information
Entry | Database: PDB / ID: 4af3 | ||||||
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Title | Human Aurora B Kinase in complex with INCENP and VX-680 | ||||||
Components |
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Keywords | TRANSFERASE/INHIBITOR / TRANSFERASE-INHIBITOR COMPLEX / AURKB | ||||||
Function / homology | Function and homology information cell cycle G2/M phase transition / positive regulation of lateral attachment of mitotic spindle microtubules to kinetochore / meiotic spindle midzone / meiotic spindle midzone assembly / central element / mitotic cytokinesis checkpoint signaling / negative regulation of cytokinesis / positive regulation of mitotic sister chromatid segregation / positive regulation of mitotic sister chromatid separation / regulation of chromosome segregation ...cell cycle G2/M phase transition / positive regulation of lateral attachment of mitotic spindle microtubules to kinetochore / meiotic spindle midzone / meiotic spindle midzone assembly / central element / mitotic cytokinesis checkpoint signaling / negative regulation of cytokinesis / positive regulation of mitotic sister chromatid segregation / positive regulation of mitotic sister chromatid separation / regulation of chromosome segregation / positive regulation of mitotic cytokinesis / mitotic sister chromatid biorientation / metaphase chromosome alignment / positive regulation of microtubule depolymerization / abscission / mitotic spindle midzone / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / repair of mitotic kinetochore microtubule attachment defect / positive regulation of attachment of mitotic spindle microtubules to kinetochore / chromocenter / cleavage furrow formation / lateral element / condensed chromosome, centromeric region / spindle pole centrosome / chromosome passenger complex / protein localization to kinetochore / negative regulation of cGAS/STING signaling pathway / negative regulation of B cell apoptotic process / spindle organization / positive regulation of cytokinesis / mitotic spindle pole / : / positive regulation of telomere capping / mitotic cytokinesis / Regulation of MECP2 expression and activity / SUMOylation of DNA replication proteins / chromosome, centromeric region / mitotic spindle assembly / spindle midzone / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / pericentric heterochromatin / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / negative regulation of innate immune response / positive regulation of telomere maintenance via telomerase / Resolution of Sister Chromatid Cohesion / protein serine/threonine/tyrosine kinase activity / post-translational protein modification / mitotic spindle organization / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / molecular function activator activity / spindle microtubule / chromosome segregation / RHO GTPases Activate Formins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / kinase binding / kinetochore / spindle / Separation of Sister Chromatids / cellular response to UV / microtubule cytoskeleton / mitotic cell cycle / midbody / Regulation of TP53 Activity through Phosphorylation / microtubule / nuclear body / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Elkins, J.M. / Vollmar, M. / Wang, J. / Picaud, S. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / von Delft, F. / Knapp, S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: Crystal Structure of Human Aurora B in Complex with Incenp and Vx-680. Authors: Elkins, J.M. / Santaguida, S. / Musacchio, A. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4af3.cif.gz | 136.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4af3.ent.gz | 106.4 KB | Display | PDB format |
PDBx/mmJSON format | 4af3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4af3_validation.pdf.gz | 728.7 KB | Display | wwPDB validaton report |
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Full document | 4af3_full_validation.pdf.gz | 731.7 KB | Display | |
Data in XML | 4af3_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 4af3_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/4af3 ftp://data.pdbj.org/pub/pdb/validation_reports/af/4af3 | HTTPS FTP |
-Related structure data
Related structure data | 2bfxS S: Starting model for refinement |
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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: 33706.086 Da / Num. of mol.: 1 / Fragment: RESIDUES 55-344 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION IMAGE 2819846 / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q96GD4, non-specific serine/threonine protein kinase |
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#2: Protein | Mass: 8229.493 Da / Num. of mol.: 1 / Fragment: RESIDUES 835-903 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGTVL1-SGC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NQS7 |
#3: Chemical | ChemComp-VX6 / |
#4: 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: 2.03 Å3/Da / Density % sol: 39.6 % / Description: NONE |
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Crystal grow | pH: 6.15 Details: 10% W/V PEG 3350, 0.2 M KSCN, 10% ETHYLENE GLYCOL, 0.1 M BIS-TRISPROPANE PH 6.15 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.976 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 11, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→19.58 Å / Num. obs: 9289 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 7 % / Rmerge(I) obs: 0.936 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BFX Resolution: 2.75→69.41 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.913 / SU B: 34.154 / SU ML: 0.332 / Cross valid method: THROUGHOUT / ESU R Free: 0.388 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 56.938 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→69.41 Å
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