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- PDB-2rsv: Solution structure of human full-length vaccinia related kinase 1... -

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Basic information

Entry
Database: PDB / ID: 2rsv
TitleSolution structure of human full-length vaccinia related kinase 1 (VRK1)
ComponentsSerine/threonine-protein kinase VRK1
KeywordsTRANSFERASE / VRK / kinase
Function / homology
Function and homology information


histone H2AX kinase activity / Golgi disassembly / Cajal body organization / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / histone H3S10 kinase activity / regulation of neuron migration / Initiation of Nuclear Envelope (NE) Reformation ...histone H2AX kinase activity / Golgi disassembly / Cajal body organization / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / histone H3S10 kinase activity / regulation of neuron migration / Initiation of Nuclear Envelope (NE) Reformation / Golgi stack / nucleosomal DNA binding / Cajal body / neuron projection development / kinase activity / protein autophosphorylation / histone binding / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / chromatin remodeling / cell division / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / protein kinase binding / chromatin / nucleolus / signal transduction / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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. ...: / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Serine/threonine-protein kinase VRK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model1
AuthorsKoshiba, S. / Tochio, N. / Yokoyama, J. / Kigawa, T.
CitationJournal: To be Published
Title: A strategy for structure determination of large molecular weight protein using isotope labeling methodology with cell-free protein systhesis: application to 45 kDa human vaccinia related kianse 1 (VRK1)
Authors: Koshiba, S. / Tochio, N. / Yokoyama, J. / Yoon, H. / Kigawa, T.
History
DepositionJul 12, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 4, 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 / 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 1.2May 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

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase VRK1


Theoretical massNumber of molelcules
Total (without water)46,0721
Polymers46,0721
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Serine/threonine-protein kinase VRK1 / Vaccinia-related kinase 1


Mass: 46071.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VRK1 / Production host: cell-free synthesis (others)
References: UniProt: Q99986, 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
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1313D 13C-13C NOESY

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Sample preparation

DetailsContents: 0.4 MM [U-13C; U-15N; U-2H; 1H ILE, LEU, VAL, ALA METHYL; 1H MET METHYL,GAMMA; 1H PHE EPSILON] VRK1, 20 MM [U-2H] TRIS,100 MM SODIUM CHLORIDE, 50 MM GLUTAMIC ACID, 50 MM ARGININE, 1 MM [U- ...Contents: 0.4 MM [U-13C; U-15N; U-2H; 1H ILE, LEU, VAL, ALA METHYL; 1H MET METHYL,GAMMA; 1H PHE EPSILON] VRK1, 20 MM [U-2H] TRIS,100 MM SODIUM CHLORIDE, 50 MM GLUTAMIC ACID, 50 MM ARGININE, 1 MM [U-2H] DTT, 0.02 % SODIUM AZIDE, 90% H2O/10% D2O; 0.4 MM [U-13C; U-15N; U-2H; 1H ILE, LEU, VAL METHYL; 1H PHE, TYR EPSILON] VRK1, 20 MM [U-2H] TRIS,100 MM SODIUM CHLORIDE, 50 MM GLUTAMIC ACID, 50 MM ARGININE, 1 MM [U-2H] DTT, 0.02 % SODIUM AZIDE, 90% H2O/10% D2O; 0.4 MM [U-15N; U-2H; 13C,1H ILE, LEU, VAL METHYL; 13C,1H PHE DELTA/EPSILON/ZETA] VRK1, 20 MM [U-2H] TRIS,100 MM SODIUM CHLORIDE, 50 MM GLUTAMIC ACID, 50 MM ARGININE, 1 MM [U-2H] DTT, 0.02 % SODIUM AZIDE, 90% H2O/10% D2O; 0.4 MM SAIL-VRK1, 20 MM [U-2H] TRIS, 100 MM SODIUM CHLORIDE, 50 MM GLUTAMIC ACID, 50 MM ARGININE, 1 MM [U-2H] DTT, 0.02 % SODIUM AZIDE, 90% H2O/10% D2O;
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMentity-1[U-13C; U-15N; U-2H]1
20 mMTRIS-2[U-2H]1
100 mMsodium chloride-31
50 mMglutamic acid-41
50 mMarginine-51
1 mMDTT-6[U-2H]1
0.02 %sodium azide-71
Sample conditionsIonic strength: 120 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
AzaraBoucherprocessing
NMRViewJohnson, One Moon Scientificdata analysis
KUJIRAN.Kobayashidata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 18 / Representative conformer: 1

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