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- PDB-4af3: Human Aurora B Kinase in complex with INCENP and VX-680 -

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Basic information

Entry
Database: PDB / ID: 4af3
TitleHuman Aurora B Kinase in complex with INCENP and VX-680
Components
  • AURORA KINASE B
  • INNER CENTROMERE PROTEIN
KeywordsTRANSFERASE/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 / mitotic cytokinesis checkpoint signaling / central element / meiotic spindle midzone / negative regulation of cytokinesis / positive regulation of mitotic sister chromatid segregation / meiotic spindle midzone assembly / positive regulation of mitotic sister chromatid separation / mitotic sister chromatid biorientation ...cell cycle G2/M phase transition / positive regulation of lateral attachment of mitotic spindle microtubules to kinetochore / mitotic cytokinesis checkpoint signaling / central element / meiotic spindle midzone / negative regulation of cytokinesis / positive regulation of mitotic sister chromatid segregation / meiotic spindle midzone assembly / positive regulation of mitotic sister chromatid separation / mitotic sister chromatid biorientation / regulation of chromosome segregation / positive regulation of mitotic cytokinesis / positive regulation of microtubule depolymerization / metaphase chromosome alignment / positive regulation of mitotic cell cycle spindle assembly checkpoint / repair of mitotic kinetochore microtubule attachment defect / mitotic spindle midzone / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / chromocenter / cleavage furrow formation / lateral element / midbody abscission / condensed chromosome, centromeric region / chromosome passenger complex / protein localization to kinetochore / spindle organization / negative regulation of B cell apoptotic process / negative regulation of cGAS/STING signaling pathway / mitotic spindle pole / positive regulation of cytokinesis / positive regulation of telomere maintenance / mitotic cytokinesis / SUMOylation of DNA replication proteins / Regulation of MECP2 expression and activity / chromosome, centromeric region / mitotic spindle assembly / spindle midzone / pericentric heterochromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / protein serine/threonine/tyrosine kinase activity / post-translational protein modification / Resolution of Sister Chromatid Cohesion / negative regulation of innate immune response / molecular function activator activity / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / mitotic spindle organization / 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 / kinetochore / spindle / kinase binding / spindle pole / Separation of Sister Chromatids / cellular response to UV / mitotic cell cycle / microtubule cytoskeleton / midbody / Regulation of TP53 Activity through Phosphorylation / microtubule / non-specific serine/threonine protein kinase / nuclear body / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2230 / Inner centromere protein, ARK-binding domain / Chromosome passenger complex (CPC) protein INCENP N-terminal / Inner centromere protein, ARK binding region / Chromosome passenger complex (CPC) protein INCENP N terminal / Aurora kinase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2230 / Inner centromere protein, ARK-binding domain / Chromosome passenger complex (CPC) protein INCENP N-terminal / Inner centromere protein, ARK binding region / Chromosome passenger complex (CPC) protein INCENP N terminal / Aurora kinase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-VX6 / Aurora kinase B / Inner centromere protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsElkins, J.M. / Vollmar, M. / Wang, J. / Picaud, S. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / von Delft, F. / Knapp, S.
CitationJournal: 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
DepositionJan 16, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references / Structure summary
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AURORA KINASE B
D: INNER CENTROMERE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4003
Polymers41,9362
Non-polymers4651
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-28.4 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.145, 80.145, 92.542
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein AURORA KINASE B / AURORA 1 / AURORA B / AURORA- AND IPL1-LIKE MIDBODY-ASSOCIATED PROTEIN 1 / AIM-1 / AURORA/IPL1- ...AURORA 1 / AURORA B / AURORA- AND IPL1-LIKE MIDBODY-ASSOCIATED PROTEIN 1 / AIM-1 / AURORA/IPL1-RELATED KINASE 2 / ARK-2 / AURORA-RELATED KINASE 2 / STK-1 / SERINE/THREONINE 12 -PROTEIN KINASE SERINE/THREONINE-PROTEIN KINASE 5 / SERINE/THREONINE-PROTEIN KINASE AURORA-B


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
#2: Protein INNER CENTROMERE PROTEIN / INCENP


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 / CYCLOPROPANECARBOXYLIC ACID {4-[4-(4-METHYL-PIPERAZIN-1-YL)-6-(5-METHYL-2H-PYRAZOL-3-YLAMINO)-PYRIMIDIN-2-YLSULFANYL]-PHENYL}-AMIDE


Mass: 464.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H28N8OS / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.6 % / Description: NONE
Crystal growpH: 6.15
Details: 10% W/V PEG 3350, 0.2 M KSCN, 10% ETHYLENE GLYCOL, 0.1 M BIS-TRISPROPANE PH 6.15

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.75→2.9 Å / Redundancy: 7 % / Rmerge(I) obs: 0.936 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
Aimlessdata scaling
SAWAYAANISOTROPY SERVERdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BFX

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
RfactorNum. reflection% reflectionSelection details
Rfree0.26438 452 4.9 %RANDOM
Rwork0.20477 ---
obs0.20776 8815 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.938 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å21.12 Å20 Å2
2--2.23 Å20 Å2
3----3.35 Å2
Refinement stepCycle: LAST / Resolution: 2.75→69.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2363 0 33 31 2427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022462
X-RAY DIFFRACTIONr_bond_other_d0.0020.021683
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.9893348
X-RAY DIFFRACTIONr_angle_other_deg0.9723.0064094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0315293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01623.304112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19315400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.751517
X-RAY DIFFRACTIONr_chiral_restr0.0640.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212705
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02505
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 26 -
Rwork0.32 583 -
obs--99.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7221.48520.05294.49210.87752.8008-0.16570.1804-0.053-0.07550.11010.18620.1124-0.04010.05570.2181-0.03240.01240.1658-0.0190.2113.6707-20.893-7.7527
219.07533.7427-12.40424.524-3.272414.69350.0857-0.51270.7908-0.3687-0.6948-0.7444-0.03450.73680.60910.2749-0.01410.13810.2070.10250.41514.9268-23.960612.1067
33.6031-1.41231.63924.1833-1.874710.0127-0.1491-0.1076-0.08820.03960.10260.007-0.49660.02570.04650.1259-0.0620.02230.04750.00690.091523.7511-4.69177.3006
41.40741.20210.18595.2218-1.62624.12380.12820.36130.0108-0.42230.09730.5146-0.18550.0492-0.22550.3837-0.0615-0.05460.3688-0.03040.25679.4757-23.0102-17.7703
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A70 - 217
2X-RAY DIFFRACTION2A218 - 250
3X-RAY DIFFRACTION3A251 - 338
4X-RAY DIFFRACTION4D840 - 882

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