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- PDB-2m9x: Solution NMR Structure of Microtubule-associated serine/threonine... -

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Basic information

Entry
Database: PDB / ID: 2m9x
TitleSolution NMR Structure of Microtubule-associated serine/threonine-protein kinase 1 from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR9151A
ComponentsMicrotubule-associated serine/threonine-protein kinase 1
KeywordsTRANSFERASE / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


cytoskeleton organization / brain development / microtubule binding / cytoskeleton / non-specific serine/threonine protein kinase / intracellular signal transduction / neuron projection / axon / protein phosphorylation / protein serine kinase activity ...cytoskeleton organization / brain development / microtubule binding / cytoskeleton / non-specific serine/threonine protein kinase / intracellular signal transduction / neuron projection / axon / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / dendrite / magnesium ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
MAST3 pre-PK domain-like / Microtubule-associated serine/threonine-protein kinase, domain / Microtubule-associated serine/threonine-protein kinase, pre-PK domain superfamily / Microtubule-associated serine/threonine-protein kinase, catalytic domain / Domain of unknown function (DUF1908) / hypothetical protein mp506/mpn330, domain 1 / PDZ domain 6 / PDZ domain / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. ...MAST3 pre-PK domain-like / Microtubule-associated serine/threonine-protein kinase, domain / Microtubule-associated serine/threonine-protein kinase, pre-PK domain superfamily / Microtubule-associated serine/threonine-protein kinase, catalytic domain / Domain of unknown function (DUF1908) / hypothetical protein mp506/mpn330, domain 1 / PDZ domain 6 / PDZ domain / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Microtubule-associated serine/threonine-protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsXu, X. / Eletsky, A. / Shastry, R. / Lee, D. / Hamilton, K. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of Microtubule-associated serine/threonine-protein kinase 1 from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR9151A
Authors: Xu, X. / Eletsky, A. / Shastry, R. / Lee, D. / Hamilton, K. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Szyperski, T.
History
DepositionJun 20, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.2May 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microtubule-associated serine/threonine-protein kinase 1


Theoretical massNumber of molelcules
Total (without water)13,0401
Polymers13,0401
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Microtubule-associated serine/threonine-protein kinase 1 / Syntrophin-associated serine/threonine-protein kinase


Mass: 13039.962 Da / Num. of mol.: 1 / Fragment: UNP residues 187-287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0973, MAST1, SAST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK
References: UniProt: Q9Y2H9, 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
1212D 1H-13C CT HSQC aliphatic
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1612D 1H-13C CT HSQC aromatic
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1813D (H)CCH-TOCSY
1913D HBHA(CO)NH
11013D HN(CA)CO
11112D 1H-15N HSQC wide
11213D (H)CCH-COSYali
11313D (H)CCH-COSYaro
11422D 1H-13C HSQC methyl

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Sample preparation

Details
Solution-IDContentsSolvent system
10.508 mM [U-100% 13C; U-100% 15N] HR9151A.011, 5 mM DTT, 100 mM NaCl, 10 mM Tris-HCl pH 7.5, 0.02 % NaN3, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
20.39 mM [%5-13C; U-100% 15N] HR9151A.011, 5 mM DTT, 100 mM NaCl, 10 mM Tris-HCl pH 7.5, 0.02 % NaN3, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.508 mMHR9151A.011-1[U-100% 13C; U-100% 15N]1
5 mMDTT-21
100 mMNaCl-31
10 mMTris-HCl pH 7.5-41
0.02 %NaN3-51
50 uMDSS-61
0.39 mMHR9151A.011-7[%5-13C; U-100% 15N]2
5 mMDTT-82
100 mMNaCl-92
10 mMTris-HCl pH 7.5-102
0.02 %NaN3-112
50 uMDSS-122
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 283 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.1Huang, Tejero, Powers and Montelionerefinement
AutoAssign2.3.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.3.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
VnmrJ2.2DVariancollection
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PSVS1.4Bhattacharya, Montelionestructure validation
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichpeak picking
CARA1.8.4Keller and Wuthrichchemical shift assignment
PROSAGuntertprocessing
CSIWishart and Sykesdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure was calculated by running CYANA and ASDP in parallel using NOE-based constraints and phi and psi dihedral angle constraints derived from Talos+. Consensus peak assignments were ...Details: Structure was calculated by running CYANA and ASDP in parallel using NOE-based constraints and phi and psi dihedral angle constraints derived from Talos+. Consensus peak assignments were selected and used in iterative refinement with CYANA. The 20 conformers out of 100 with the lowest target function were further refined by simulated annealing in explicit water bath using the program CNS with PARAM19 force field.
NMR constraintsNOE constraints total: 831 / NOE intraresidue total count: 227 / NOE long range total count: 192 / NOE medium range total count: 130 / NOE sequential total count: 186 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 65 / Protein psi angle constraints total count: 65
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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