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- PDB-2lav: NMR solution structure of human Vaccinia-Related Kinase 1 -

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Basic information

Entry
Database: PDB / ID: 2lav
TitleNMR solution structure of human Vaccinia-Related Kinase 1
ComponentsVaccinia-related kinase 1
KeywordsTRANSFERASE / VRK1 / SERINE/THREONINE-PROTEIN KINASE / MITOSIS / CELL CYCLE
Function / homology
Function and homology information


Golgi disassembly / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation / histone H3S10 kinase activity / kinase activity / histone binding ...Golgi disassembly / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation / histone H3S10 kinase activity / kinase activity / histone binding / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / cell division / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / nucleolus / protein kinase binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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. ...Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase VRK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsShin, J. / Yoon, H.S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: NMR Solution Structure of Human Vaccinia-related Kinase 1 (VRK1) Reveals the C-terminal Tail Essential for Its Structural Stability and Autocatalytic Activity.
Authors: Shin, J. / Chakraborty, G. / Bharatham, N. / Kang, C. / Tochio, N. / Koshiba, S. / Kigawa, T. / Kim, W. / Kim, K.T. / Yoon, H.S.
History
DepositionMar 21, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 4, 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
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
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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vaccinia-related kinase 1


Theoretical massNumber of molelcules
Total (without water)41,4161
Polymers41,4161
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 41415.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VRK1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q99986, non-specific serine/threonine protein kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: NA
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N HSQC
1312D 1H-15N HSQC
1413D HN(CA)CB
1513D HN(CA)CB
1613D HN(COCA)CB
1713D HN(COCA)CB
1813D HNCO
1913D HNCA
11013D HN(CO)CA
11113D HN(CA)CO
11213D 1H-15N NOESY
11313D 1H-15N NOESY
11423D 1H-13C NOESY
11523D 1H-13C NOESY
11623D (H)CCH-TOCSY
11723D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3-0.5 mM [U-100% 13C; U-100% 15N; U-80% 2H] Vaccinia Related-Kinase 1, 0.3-0.5 mM [U-100% 15N; U-50% 2H] Vaccinia Related-Kinase 1, 0.1-0.2 mM [U-100% 15N] Vaccinia Related-Kinase 1, 90% H2O/10% D2O90% H2O/10% D2O
20.3-0.5 mM [U-100% 13C; U-100% 15N; U-70% 2H] Vaccinia Related-Kinase 1, 0.3-0.5 mM [13C;15N]-Val,Ile,Leu; [U-100% 2H] Vaccinia Related-Kinase 1, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMVaccinia Related-Kinase 1-1[U-100% 13C; U-100% 15N; U-80% 2H]0.3-0.51
mMVaccinia Related-Kinase 1-2[U-100% 15N; U-50% 2H]0.3-0.51
mMVaccinia Related-Kinase 1-3[U-100% 15N]0.1-0.21
90 %H2O-41
10 %D2O-51
mMVaccinia Related-Kinase 1-6[U-100% 13C; U-100% 15N; U-70% 2H]0.3-0.52
mMVaccinia Related-Kinase 1-7[13C;15N]-Val,Ile,Leu; [U-100% 2H]0.3-0.52
100 %D2O-82
Sample conditionsIonic strength: 20 / pH: 6.8 / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
CYANAGuntert, Mumenthaler and Wuthrichinitial structure calculation
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
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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