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- PDB-3si5: Kinetochore-BUBR1 kinase complex -

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Basic information

Entry
Database: PDB / ID: 3si5
TitleKinetochore-BUBR1 kinase complex
Components
  • Mitotic checkpoint serine/threonine-protein kinase BUB1 beta
  • Protein CASC5
KeywordsCELL CYCLE / BUBR1-Blinkin complex / mitotic checkpoint / BUBR1 / Blinkin/KNL1 / chromosome segregation
Function / homology
Function and homology information


Knl1/Spc105 complex / positive regulation of meiosis I spindle assembly checkpoint / homologous chromosome orientation in meiotic metaphase I / mitotic checkpoint complex / acrosome assembly / regulation of mitotic cell cycle spindle assembly checkpoint / meiotic sister chromatid cohesion, centromeric / attachment of spindle microtubules to kinetochore / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins ...Knl1/Spc105 complex / positive regulation of meiosis I spindle assembly checkpoint / homologous chromosome orientation in meiotic metaphase I / mitotic checkpoint complex / acrosome assembly / regulation of mitotic cell cycle spindle assembly checkpoint / meiotic sister chromatid cohesion, centromeric / attachment of spindle microtubules to kinetochore / 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 / protein localization to kinetochore / mitotic spindle assembly checkpoint signaling / mitotic sister chromatid segregation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Deposition of new CENPA-containing nucleosomes at the centromere / Resolution of Sister Chromatid Cohesion / APC-Cdc20 mediated degradation of Nek2A / acrosomal vesicle / RHO GTPases Activate Formins / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / spindle / kinetochore / Separation of Sister Chromatids / nuclear body / non-specific serine/threonine protein kinase / protein kinase activity / cell division / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / apoptotic process / perinuclear region of cytoplasm / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #430 / Knl1, C-terminal RWD domain / Knl1 RWD C-terminal domain / Kinetochore scaffold 1 / KNL1 MELT repeat / MELT motif / Mad3/Bub1 homology region 1 / Mitotic spindle checkpoint protein Bub1/Mad3 / Mad3/BUB1 homology region 1 / BUB1 N-terminal domain profile. ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #430 / Knl1, C-terminal RWD domain / Knl1 RWD C-terminal domain / Kinetochore scaffold 1 / KNL1 MELT repeat / MELT motif / 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
Mitotic checkpoint serine/threonine-protein kinase BUB1 beta / Kinetochore scaffold 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBlundell, T.L. / Chirgadze, D.Y. / Bolanos-Garcia, V.M.
CitationJournal: Structure / Year: 2011
Title: Structure of a Blinkin-BUBR1 Complex Reveals an Interaction Crucial for Kinetochore-Mitotic Checkpoint Regulation via an Unanticipated Binding Site.
Authors: Bolanos-Garcia, V.M. / Lischetti, T. / Matak-Vinkovic, D. / Cota, E. / Simpson, P.J. / Chirgadze, D.Y. / Spring, D.R. / Robinson, C.V. / Nilsson, J. / Blundell, T.L.
History
DepositionJun 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
B: Mitotic checkpoint serine/threonine-protein kinase BUB1 beta
X: Protein CASC5
Y: Protein CASC5


Theoretical massNumber of molelcules
Total (without water)46,4714
Polymers46,4714
Non-polymers00
Water4,504250
1
A: Mitotic checkpoint serine/threonine-protein kinase BUB1 beta
X: Protein CASC5


Theoretical massNumber of molelcules
Total (without water)23,2362
Polymers23,2362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-7 kcal/mol
Surface area10070 Å2
MethodPISA
2
B: Mitotic checkpoint serine/threonine-protein kinase BUB1 beta
Y: Protein CASC5


Theoretical massNumber of molelcules
Total (without water)23,2362
Polymers23,2362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-10 kcal/mol
Surface area9690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.398, 40.143, 75.391
Angle α, β, γ (deg.)90.00, 91.38, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-280-

HOH

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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


Mass: 20578.621 Da / Num. of mol.: 2 / Fragment: UNP residues 67-220
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BUB1B, BUBR1, MAD3L, SSK1 / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O60566, non-specific serine/threonine protein kinase
#2: Protein/peptide Protein CASC5 / ALL1-fused gene from chromosome 15q14 protein / AF15q14 / Bub-linking kinetochore protein / Blinkin ...ALL1-fused gene from chromosome 15q14 protein / AF15q14 / Bub-linking kinetochore protein / Blinkin / Cancer susceptibility candidate gene 5 protein / Cancer/testis antigen 29 / CT29 / Kinetochore-null protein 1 / Protein D40/AF15q14


Mass: 2657.010 Da / Num. of mol.: 2 / Fragment: UNP residues 234-252
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASC5, KIAA1570, KNL1 / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8NG31
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.02 Å3/Da / Density % sol: 39.25 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15% PEG 6000, 0.1M Magnesium Acetate, 0.1M Sodium Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Dec 5, 2010 / Details: HELIOS MX Cu X-RAY OPTICS FOR X8 PROTEUM/MICROSTAR
RadiationMonochromator: HELIOS MX mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→38.2 Å / Num. all: 19283 / Num. obs: 19266 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.119 / Rsym value: 0.119 / Net I/σ(I): 14.1
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2379 / Rsym value: 0.465 / % possible all: 100

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Processing

Software
NameVersionClassification
PROTEUM2data collection
AMoREphasing
REFMAC5.5.0109refinement
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WVI

2wvi


Resolution: 2.2→38.2 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.902 / SU B: 13.612 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24665 985 5.1 %RANDOM
Rwork0.19343 ---
all0.19626 18292 --
obs0.19626 18278 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.773 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2756 0 0 250 3006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222866
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.933875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1135340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.50123.908174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14115491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6991528
X-RAY DIFFRACTIONr_chiral_restr0.0740.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212290
X-RAY DIFFRACTIONr_mcbond_it0.6031.51667
X-RAY DIFFRACTIONr_mcangle_it1.13322658
X-RAY DIFFRACTIONr_scbond_it1.65531199
X-RAY DIFFRACTIONr_scangle_it2.7334.51211
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 70 -
Rwork0.2 1347 -
obs--100 %
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)
10.32430.1350.47370.13350.16890.66270.0106-0.01380.0050.0193-0.02570.00160.0243-0.03260.01520.1553-0.0096-0.00580.13850.00030.160414.7898-0.173231.4405
20.30990.2216-0.55140.1606-0.40611.49720.0035-0.0092-0.0182-0.0026-0.0290.0019-0.0591-0.02150.02550.16-0.0028-0.01010.1301-0.00430.149947.68589.779213.6067
310.8371-5.6074-0.28189.12631.70820.03470.22740.3935-0.1987-0.6638-0.17280.1254-0.16530.139-0.05460.1951-0.0330.0030.2051-0.04240.100119.097.707417.5814
417.51190.8577-1.946623.326915.491810.90890.4008-0.0045-0.1507-0.63290.06630.2502-0.2076-1.3103-0.46710.0294-0.208-0.11670.89690.45030.162534.2235.73066.0214
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A54 - 205
2X-RAY DIFFRACTION2B55 - 203
3X-RAY DIFFRACTION3X2 - 19
4X-RAY DIFFRACTION4Y6 - 18

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