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- PDB-4c2w: Crystal structure of Aurora B in complex with AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 4c2w
TitleCrystal structure of Aurora B in complex with AMP-PNP
Components
  • AURORA KINASE B-A
  • INNER CENTROMERE PROTEIN A
KeywordsTRANSFERASE
Function / homology
Function and homology information


mitotic cytokinesis checkpoint signaling / meiotic spindle midzone / negative regulation of cytokinesis / positive regulation of mitotic sister chromatid segregation / meiotic spindle midzone assembly / metaphase chromosome alignment / mitotic spindle midzone assembly / cleavage furrow formation / midbody abscission / chromosome passenger complex ...mitotic cytokinesis checkpoint signaling / meiotic spindle midzone / negative regulation of cytokinesis / positive regulation of mitotic sister chromatid segregation / meiotic spindle midzone assembly / metaphase chromosome alignment / mitotic spindle midzone assembly / cleavage furrow formation / midbody abscission / chromosome passenger complex / protein localization to kinetochore / histone H3S10 kinase activity / negative regulation of B cell apoptotic process / positive regulation of cytokinesis / spindle midzone / pericentric heterochromatin / mitotic cytokinesis / chromosome, centromeric region / spindle assembly / post-translational protein modification / regulation of cytokinesis / mitotic spindle organization / spindle microtubule / chromosome segregation / kinetochore / spindle / spindle pole / cellular response to UV / chromosome / midbody / microtubule / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / protein kinase binding / chromatin / negative regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2990 / 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 / Helix non-globular / Special / Phosphorylase Kinase; domain 1 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2990 / 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 / Helix non-globular / Special / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Inner centromere protein A / Aurora kinase B-A
Similarity search - Component
Biological speciesXENOPUS LAEVIS (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSessa, F. / Villa, F.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Structure of Aurora B-Incenp in Complex with Barasertib Reveals a Potential Transinhibitory Mechanism
Authors: Sessa, F. / Villa, F.
History
DepositionAug 20, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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)79,3576
Polymers78,3454
Non-polymers1,0122
Water12,647702
1
A: AURORA KINASE B-A
D: INNER CENTROMERE PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6793
Polymers39,1722
Non-polymers5061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-24.5 kcal/mol
Surface area17000 Å2
MethodPISA
2
B: AURORA KINASE B-A
C: INNER CENTROMERE PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6793
Polymers39,1722
Non-polymers5061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-19.7 kcal/mol
Surface area15990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.922, 66.656, 116.903
Angle α, β, γ (deg.)90.00, 96.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 33005.301 Da / Num. of mol.: 2 / Fragment: RESIDUES 78-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XENOPUS LAEVIS (African clawed frog) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q6DE08, non-specific serine/threonine protein kinase
#2: Protein INNER CENTROMERE PROTEIN A / XL-INCENP / XINC / XINCENP / MITOTIC PHOSPHOPROTEIN 130 / PROTEIN KINASE


Mass: 6167.122 Da / Num. of mol.: 2 / Fragment: RESIDUES 797-847
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XENOPUS LAEVIS (African clawed frog) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O13024
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 702 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.76 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→45.6 Å / Num. obs: 74825 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 30.8
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 10 / % possible all: 94

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→43.77 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.736 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19534 3738 5 %RANDOM
Rwork0.15644 ---
obs0.15841 71057 97.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.236 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.14 Å2
2--0.3 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5298 0 54 702 6054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0195542
X-RAY DIFFRACTIONr_bond_other_d0.0020.025326
X-RAY DIFFRACTIONr_angle_refined_deg2.1981.9887491
X-RAY DIFFRACTIONr_angle_other_deg1.0363.00312283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06822.565269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.924151005
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6031552
X-RAY DIFFRACTIONr_chiral_restr0.2010.2773
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216088
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021322
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 264 -
Rwork0.168 5011 -
obs--93.53 %

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