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- PDB-2wvi: Crystal Structure of the N-terminal Domain of BubR1 -

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Basic information

Entry
Database: PDB / ID: 2wvi
TitleCrystal Structure of the N-terminal Domain of BubR1
ComponentsMITOTIC CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1 BETA
KeywordsTRANSFERASE / TUMOR SUPPRESSOR / MITOTIC CHECKPOINT / TPR / KINASE / APOPTOSIS / SERINE/THREONINE-PROTEIN KINASE / CELL DIVISION / CELL CYCLE / KINETOCHORE / CYTOSKELETON
Function / homology
Function and homology information


mitotic checkpoint complex / meiotic sister chromatid cohesion, centromeric / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / metaphase/anaphase transition of mitotic cell cycle / outer kinetochore / protein localization to chromosome, centromeric region / mitotic spindle assembly checkpoint signaling / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal ...mitotic checkpoint complex / meiotic sister chromatid cohesion, centromeric / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / metaphase/anaphase transition of mitotic cell cycle / outer kinetochore / protein localization to chromosome, centromeric region / mitotic spindle assembly checkpoint signaling / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / APC-Cdc20 mediated degradation of Nek2A / Resolution of Sister Chromatid Cohesion / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / RHO GTPases Activate Formins / kinetochore / spindle / Separation of Sister Chromatids / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / ciliary basal body / cell division / protein serine kinase activity / apoptotic process / centrosome / perinuclear region of cytoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #430 / Mad3/Bub1 homology region 1 / Mitotic spindle checkpoint protein Bub1/Mad3 / Mad3/BUB1 homology region 1 / BUB1 N-terminal domain profile. / Mad3/BUB1 hoMad3/BUB1 homology region 1 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Protein kinase-like domain superfamily / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / PRASEODYMIUM ION / Mitotic checkpoint serine/threonine-protein kinase BUB1 beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsD'Arcy, S. / Davies, O.R. / Blundell, T.L. / Bolanos-Garcia, V.M.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Defining the Molecular Basis of Bubr1 Kinetochore Interactions and Anaphase-Promoting Complex/Cyclosome (Apc/C)-Cdc20 Inhibition
Authors: D'Arcy, S. / Davies, O.R. / Blundell, T.L. / Bolanos-Garcia, V.M.
History
DepositionOct 16, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: MITOTIC CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1 BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0636
Polymers19,5981
Non-polymers4655
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.796, 62.796, 90.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein MITOTIC CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1 BETA / MAD3/BUB1-RELATED PROTEIN KINASE / HBUBR1 / MITOTIC CHECKPOINT KINASE MAD3L / PROTEIN SSK1 / BUBR1


Mass: 19597.682 Da / Num. of mol.: 1 / Fragment: N-TERMINAL TPR DOMAIN, RESIDUES 57-220
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHAT4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O60566, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-PR / PRASEODYMIUM ION


Mass: 140.908 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pr
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsETHANE-1,2-DIOL (EDO): USED AS CRYOPROTECTANT PRASEODYMIUM ION (PR): ESSENTIAL FOR HIGH RESOLUTION ...ETHANE-1,2-DIOL (EDO): USED AS CRYOPROTECTANT PRASEODYMIUM ION (PR): ESSENTIAL FOR HIGH RESOLUTION OF CRYSTALS AND USED FOR PHASING

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 49 % / Description: THIS DATA SET WAS USED IN REFINEMENTS.
Crystal growpH: 8
Details: 22.5% (W/V) PEG 8000, 0.17 M TRIS PH 8.0, 0.01 M PRASEODYMIUM(III) ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.06
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 12, 2007
Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING
RadiationMonochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 1.8→46.62 Å / Num. obs: 19685 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 15.6 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 21
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 15.8 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.8→54.39 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.444 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DENSITY WAS NOT OBSERVED FOR RESIDUES 92-95. ONE ROUND OF TLS WAS CONDUCTED DURING REFINEMENT. TWO GROUPS WERE USED; RESIDUES 57-114 AND 115-220.
RfactorNum. reflection% reflectionSelection details
Rfree0.25986 1005 5.1 %RANDOM
Rwork0.22188 ---
obs0.22373 18643 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.105 Å2
Baniso -1Baniso -2Baniso -3
1-2.24 Å21.12 Å20 Å2
2--2.24 Å20 Å2
3----3.35 Å2
Refinement stepCycle: LAST / Resolution: 1.8→54.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1358 0 14 117 1489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221398
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.9451880
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.9345158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.26724.18686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.69315245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7681513
X-RAY DIFFRACTIONr_chiral_restr0.1350.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021105
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2360.2699
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2943
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3010.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0641.5827
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67921277
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7723666
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2574.5603
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: 1.8→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.346 69
Rwork0.255 1367

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