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- PDB-2lah: Solution NMR Structure of Mitotic checkpoint serine/threonine-pro... -

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Basic information

Entry
Database: PDB / ID: 2lah
TitleSolution NMR Structure of Mitotic checkpoint serine/threonine-protein kinase BUB1 N-terminal domain from Homo sapiens, Northeast Structural Genomics Consortium Target HR5460A (Methods Development)
ComponentsMitotic checkpoint serine/threonine-protein kinase BUB1
KeywordsCELL CYCLE / APOPTOSIS / Structural Genomics / Protein NMR / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / Target HR5460A / PSI-Biology / Protein Structure Initiative / Methods Development
Function / homology
Function and homology information


histone H2A kinase activity / positive regulation of maintenance of mitotic sister chromatid cohesion, centromeric / regulation of sister chromatid cohesion / regulation of chromosome segregation / meiotic sister chromatid cohesion, centromeric / outer kinetochore / 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 ...histone H2A kinase activity / positive regulation of maintenance of mitotic sister chromatid cohesion, centromeric / regulation of sister chromatid cohesion / regulation of chromosome segregation / meiotic sister chromatid cohesion, centromeric / outer kinetochore / 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 / Resolution of Sister Chromatid Cohesion / chromosome segregation / RHO GTPases Activate Formins / kinetochore / Separation of Sister Chromatids / non-specific serine/threonine protein kinase / protein kinase activity / cell division / phosphorylation / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / apoptotic process / nucleoplasm / ATP binding / membrane / nucleus / cytosol
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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...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 / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, torsion angle dynamics, simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsLiu, G. / Xiao, R. / Lee, H. / Hamilton, K. / Acton, T.B. / Ciccosanti, C. / Everett, J.K. / Shastry, R.T. / Huang, Y.J. / Montelione, G.T. ...Liu, G. / Xiao, R. / Lee, H. / Hamilton, K. / Acton, T.B. / Ciccosanti, C. / Everett, J.K. / Shastry, R.T. / Huang, Y.J. / Montelione, G.T. / Northeast Structural Genomics Consortium, n. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target HR5460A
Authors: Liu, G. / Shastry, R. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T.
History
DepositionMar 14, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Mitotic checkpoint serine/threonine-protein kinase BUB1


Theoretical massNumber of molelcules
Total (without water)19,2091
Polymers19,2091
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Mitotic checkpoint serine/threonine-protein kinase BUB1 / hBUB1 / BUB1A


Mass: 19209.490 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BUB1, BUB1L / Plasmid: pET 14-15C / Production host: Escherichia coli (E. coli)
References: UniProt: O43683, non-specific serine/threonine protein kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D 1H-13C arom NOESY
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1822D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.164 mM [U-100% 13C; U-100% 15N] HR5460A, 95% H2O/5% D2O95% H2O/5% D2O
21.033 mM [U-10% 13C; U-100% 15N] HR5460A, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.164 mMHR5460A-1[U-100% 13C; U-100% 15N]1
1.033 mMHR5460A-2[U-10% 13C; U-100% 15N]2
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinemen,structure solution,geometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement,geometry optimization,structure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis,refinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis,chemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis,peak picking,chemical shift assignment
TopSpinBruker Biospincollection
VnmrJVariancollection
SparkyGoddarddata analysis
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
CYANArefinement
CNSrefinement
RefinementMethod: distance geometry, torsion angle dynamics, simulated annealing, molecular dynamics
Software ordinal: 1
NMR constraintsNOE constraints total: 4690
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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