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- PDB-2bfy: Complex of Aurora-B with INCENP and Hesperadin. -

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Basic information

Entry
Database: PDB / ID: 2bfy
TitleComplex of Aurora-B with INCENP and Hesperadin.
Components
  • AURORA KINASE B-A
  • INNER CENTROMERE PROTEIN A
KeywordsTRANSFERASE / KINASE / MITOSIS / INHIBITION / TRANSFERASE COMPLEX
Function / homology
Function and homology information


meiotic spindle midzone / mitotic cytokinesis checkpoint signaling / negative regulation of cytokinesis / positive regulation of mitotic sister chromatid segregation / meiotic spindle midzone assembly / metaphase chromosome alignment / abscission / mitotic spindle midzone assembly / cleavage furrow formation / spindle pole centrosome ...meiotic spindle midzone / mitotic cytokinesis checkpoint signaling / negative regulation of cytokinesis / positive regulation of mitotic sister chromatid segregation / meiotic spindle midzone assembly / metaphase chromosome alignment / abscission / mitotic spindle midzone assembly / cleavage furrow formation / spindle pole centrosome / histone H3S10 kinase activity / chromosome passenger complex / protein localization to kinetochore / negative regulation of B cell apoptotic process / positive regulation of cytokinesis / chromosome, centromeric region / mitotic cytokinesis / spindle assembly / spindle midzone / pericentric heterochromatin / post-translational protein modification / chromosome segregation / spindle microtubule / kinetochore / spindle / cellular response to UV / chromosome / midbody / microtubule / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / chromatin / protein kinase binding / negative regulation of transcription by RNA polymerase II / ATP binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site ...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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-H1N / Inner centromere protein A / Aurora kinase B-A
Similarity search - Component
Biological speciesXENOPUS LAEVIS (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSessa, F. / Mapelli, M. / Ciferri, C. / Tarricone, C. / Areces, L.B. / Schneider, T.R. / Stukenberg, P.T. / Musacchio, A.
CitationJournal: Mol.Cell / Year: 2005
Title: Mechanism of Aurora B Activation by Incenp and Inhibition by Hesperadin
Authors: Sessa, F. / Mapelli, M. / Ciferri, C. / Tarricone, C. / Areces, L.B. / Schneider, T.R. / Stukenberg, P.T. / Musacchio, A.
History
DepositionDec 15, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 20, 2015Group: Structure summary
Revision 1.3Dec 13, 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_conn / 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_conn.pdbx_leaving_atom_flag / _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-A
B: AURORA KINASE B-A
C: INNER CENTROMERE PROTEIN A
D: INNER CENTROMERE PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1466
Polymers77,1134
Non-polymers1,0332
Water6,900383
1
A: AURORA KINASE B-A
D: INNER CENTROMERE PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0733
Polymers38,5572
Non-polymers5171
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-29.8 kcal/mol
Surface area15590 Å2
MethodPISA
2
B: AURORA KINASE B-A
C: INNER CENTROMERE PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0733
Polymers38,5572
Non-polymers5171
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-32.2 kcal/mol
Surface area15970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.945, 67.044, 116.462
Angle α, β, γ (deg.)90.00, 96.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AURORA KINASE B-A / LOC398457 PROTEIN / AURORA-B / AURORA/IPL1-RELATED KINASE 2-A / AIRK2-A / XAIRK2-A / ...LOC398457 PROTEIN / AURORA-B / AURORA/IPL1-RELATED KINASE 2-A / AIRK2-A / XAIRK2-A / SERINE/THREONINE-PROTEIN KINASE 12-A / SERINE/THREONINE-PROTEIN KINASE AURORA-B-A / XAURORA-B


Mass: 33579.949 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 78-361 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: PHOSPHORYLATED ON T248 / Source: (gene. exp.) XENOPUS LAEVIS (African clawed frog) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q6DE08, non-specific serine/threonine protein kinase
#2: Protein/peptide INNER CENTROMERE PROTEIN A / INCENP / XL-INCENP / XINC / XINCENP / MITOTIC PHOSPHOPROTEIN 130


Mass: 4976.640 Da / Num. of mol.: 2 / Fragment: RESIDUES 798-840
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XENOPUS LAEVIS (African clawed frog) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O13024
#3: Chemical ChemComp-H1N / N-[2-OXO-3-((E)-PHENYL{[4-(PIPERIDIN-1-YLMETHYL)PHENYL]IMINO}METHYL)-2,6-DIHYDRO-1H-INDOL-5-YL]ETHANESULFONAMIDE / HESPERADIN


Mass: 516.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H32N4O3S / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE CHAINS A, B GLY 96 VAL

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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: 2.3 Å3/Da / Density % sol: 45 %
Crystal growDetails: 0.1 M BIS TRIS PROPANE PH 6.6, 18% PEG3350

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 67250 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 25
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.02 / Mean I/σ(I) obs: 2.9 / % possible all: 79

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OL5

1ol5


Resolution: 1.8→19.34 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1263449.93 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.226 3270 5.1 %RANDOM
Rwork0.203 ---
obs0.203 64077 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.519 Å2 / ksol: 0.407683 e/Å3
Displacement parametersBiso mean: 30.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å2-1.39 Å2
2--6.78 Å20 Å2
3----7.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5179 0 74 383 5636
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.31
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.283 519 5.3 %
Rwork0.224 9313 -
obs--90.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2TPO.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMTPO.TOP
X-RAY DIFFRACTION4HESPERIDIN.PARAMHESPERIDIN.TOP

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