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- PDB-4a1g: The crystal structure of the human Bub1 TPR domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4a1g
TitleThe crystal structure of the human Bub1 TPR domain in complex with the KI motif of Knl1
Components
  • MITOTIC CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1
  • PROTEIN CASC5
KeywordsCELL CYCLE / TRANSFERASE / SPINDLE ASSEMBLY CHECKPOINT / MITOSIS / TPR REPEAT / KNL1 / KMN NETWORK
Function / homology
Function and homology information


histone H2A kinase activity / positive regulation of maintenance of mitotic sister chromatid cohesion, centromeric / Knl1/Spc105 complex / positive regulation of meiosis I spindle assembly checkpoint / homologous chromosome orientation in meiotic metaphase I / regulation of sister chromatid cohesion / regulation of chromosome segregation / acrosome assembly / meiotic sister chromatid cohesion, centromeric / regulation of mitotic cell cycle spindle assembly checkpoint ...histone H2A kinase activity / positive regulation of maintenance of mitotic sister chromatid cohesion, centromeric / Knl1/Spc105 complex / positive regulation of meiosis I spindle assembly checkpoint / homologous chromosome orientation in meiotic metaphase I / regulation of sister chromatid cohesion / regulation of chromosome segregation / acrosome assembly / meiotic sister chromatid cohesion, centromeric / regulation of mitotic cell cycle spindle assembly checkpoint / attachment of spindle microtubules to kinetochore / outer kinetochore / 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 / acrosomal vesicle / chromosome segregation / RHO GTPases Activate Formins / kinetochore / Separation of Sister Chromatids / microtubule binding / nuclear body / non-specific serine/threonine protein kinase / protein kinase activity / cell division / intracellular membrane-bounded organelle / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / nucleoplasm / ATP binding / membrane / nucleus / cytosol
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #430 / Kinetochore scaffold 1 / Knl1, C-terminal RWD domain / KNL1 MELT repeat / Knl1 RWD C-terminal domain / 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 / Kinetochore scaffold 1 / Knl1, C-terminal RWD domain / KNL1 MELT repeat / Knl1 RWD C-terminal domain / 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 / 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 / Mainly Alpha
Similarity search - Domain/homology
Mitotic checkpoint serine/threonine-protein kinase BUB1 / Kinetochore scaffold 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKrenn, V. / Wehenkel, A. / Li, X. / Santaguida, S. / Musacchio, A.
CitationJournal: J.Cell Biol. / Year: 2012
Title: Structural Analysis Reveals Features of the Spindle Checkpoint Kinase Bub1-Kinetochore Subunit Knl1 Interaction.
Authors: Krenn, V. / Wehenkel, A. / Li, X. / Santaguida, S. / Musacchio, A.
History
DepositionSep 15, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Data collection / Source and taxonomy / Category: diffrn_detector / entity_src_gen
Item: _diffrn_detector.type / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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
B: MITOTIC CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1
C: MITOTIC CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1
D: MITOTIC CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1
E: PROTEIN CASC5
F: PROTEIN CASC5
G: PROTEIN CASC5
H: PROTEIN CASC5


Theoretical massNumber of molelcules
Total (without water)96,1328
Polymers96,1328
Non-polymers00
Water2,162120
1
A: MITOTIC CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1
E: PROTEIN CASC5


Theoretical massNumber of molelcules
Total (without water)24,0332
Polymers24,0332
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-7.6 kcal/mol
Surface area8580 Å2
MethodPISA
2
B: MITOTIC CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1
F: PROTEIN CASC5


Theoretical massNumber of molelcules
Total (without water)24,0332
Polymers24,0332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-8.4 kcal/mol
Surface area9240 Å2
MethodPISA
3
C: MITOTIC CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1
G: PROTEIN CASC5


Theoretical massNumber of molelcules
Total (without water)24,0332
Polymers24,0332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-6.7 kcal/mol
Surface area9330 Å2
MethodPISA
4
D: MITOTIC CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1
H: PROTEIN CASC5


Theoretical massNumber of molelcules
Total (without water)24,0332
Polymers24,0332
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-9.1 kcal/mol
Surface area9110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.279, 130.969, 74.956
Angle α, β, γ (deg.)90.00, 110.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
MITOTIC CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1 / HBUB1 / BUB1A / BUB1


Mass: 18121.299 Da / Num. of mol.: 4 / Fragment: TPR DOMAIN, RESIDUES 1-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-2RBS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: O43683, non-specific serine/threonine protein kinase
#2: Protein
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 / KNL1


Mass: 5911.757 Da / Num. of mol.: 4 / Fragment: KI MOTIF, RESIDUES 150-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA / References: UniProt: Q8NG31
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.03 Å3/Da / Density % sol: 59.5 % / Description: NONE
Crystal growpH: 6 / Details: 1.25-1.3 M NA MALONATE, PH 6.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 7, 2009
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.6→65 Å / Num. obs: 32541 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.7
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ESL

3esl


Resolution: 2.6→61.983 Å / SU ML: 0.38 / σ(F): 1.38 / Phase error: 24.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2436 1653 5.1 %
Rwork0.1859 --
obs0.1889 32540 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.497 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1026 Å20 Å20.3248 Å2
2--0.8728 Å20 Å2
3----1.9754 Å2
Refinement stepCycle: LAST / Resolution: 2.6→61.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5377 0 0 120 5497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095522
X-RAY DIFFRACTIONf_angle_d1.1737480
X-RAY DIFFRACTIONf_dihedral_angle_d21.9491958
X-RAY DIFFRACTIONf_chiral_restr0.089782
X-RAY DIFFRACTIONf_plane_restr0.005969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.67660.31171490.25582591X-RAY DIFFRACTION100
2.6766-2.7630.3021420.24242576X-RAY DIFFRACTION99
2.763-2.86170.28111300.22562570X-RAY DIFFRACTION99
2.8617-2.97630.33151510.23052585X-RAY DIFFRACTION99
2.9763-3.11180.30291400.2242614X-RAY DIFFRACTION99
3.1118-3.27580.28841430.21752561X-RAY DIFFRACTION99
3.2758-3.4810.26211270.18092572X-RAY DIFFRACTION99
3.481-3.74980.19221140.16342600X-RAY DIFFRACTION99
3.7498-4.12710.23161430.15212553X-RAY DIFFRACTION98
4.1271-4.72410.20191520.15872548X-RAY DIFFRACTION98
4.7241-5.95110.20291360.16512573X-RAY DIFFRACTION98
5.9511-62.00010.21261260.16732544X-RAY DIFFRACTION95

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