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- PDB-3kn6: Crystal structure of the C-terminal kinase domain of MSK1 -

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Basic information

Entry
Database: PDB / ID: 3kn6
TitleCrystal structure of the C-terminal kinase domain of MSK1
ComponentsRibosomal protein S6 kinase alpha-5
KeywordsTRANSFERASE / KINASE / AMP-PNP / MSK1 / MSK / ATP-BINDING / METAL-BINDING / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE
Function / homology
Function and homology information


histone H3S28 kinase activity / histone H2AS1 kinase activity / positive regulation of CREB transcription factor activity / CREB phosphorylation / histone H3S10 kinase activity / interleukin-1-mediated signaling pathway / negative regulation of cytokine production / regulation of postsynapse organization / ERK/MAPK targets / Recycling pathway of L1 ...histone H3S28 kinase activity / histone H2AS1 kinase activity / positive regulation of CREB transcription factor activity / CREB phosphorylation / histone H3S10 kinase activity / interleukin-1-mediated signaling pathway / negative regulation of cytokine production / regulation of postsynapse organization / ERK/MAPK targets / Recycling pathway of L1 / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / post-translational protein modification / axon guidance / positive regulation of NF-kappaB transcription factor activity / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / intracellular signal transduction / inflammatory response / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Ribosomal protein S6 kinase II / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...Ribosomal protein S6 kinase II / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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
Ribosomal protein S6 kinase alpha-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsD'Angelo, I. / Malakhova, M. / Dong, Z.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: The crystal structure of the active form of the C-terminal kinase domain of mitogen- and stress-activated protein kinase 1.
Authors: Malakhova, M. / D'Angelo, I. / Kim, H.G. / Kurinov, I. / Bode, A.M. / Dong, Z.
History
DepositionNov 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosomal protein S6 kinase alpha-5
B: Ribosomal protein S6 kinase alpha-5


Theoretical massNumber of molelcules
Total (without water)74,0112
Polymers74,0112
Non-polymers00
Water3,765209
1
A: Ribosomal protein S6 kinase alpha-5


Theoretical massNumber of molelcules
Total (without water)37,0061
Polymers37,0061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribosomal protein S6 kinase alpha-5


Theoretical massNumber of molelcules
Total (without water)37,0061
Polymers37,0061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.386, 91.739, 134.945
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribosomal protein S6 kinase alpha-5 / Nuclear mitogen- and stress-activated protein kinase 1 / 90 kDa ribosomal protein S6 kinase 5 / RSK- ...Nuclear mitogen- and stress-activated protein kinase 1 / 90 kDa ribosomal protein S6 kinase 5 / RSK-like protein kinase / RSKL


Mass: 37005.500 Da / Num. of mol.: 2 / Fragment: residues 414-738
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSK1, RPS6KA5 / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODON PLUS (DE3)-RILP
References: UniProt: O75582, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.15 Å3/Da / Density % sol: 42.76 %
Crystal growpH: 7.5 / Details: PH 7.5, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→45.87 Å / Num. obs: 43534 / % possible obs: 93 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 31.4
Reflection shellResolution: 2→2.15 Å / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.441 / % possible all: 75

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QR8

2qr8


Resolution: 2→45.87 Å / SU ML: 0.32 / σ(F): 1.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.263 2183 5.02 %
Rwork0.216 --
obs0.219 43443 52.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.67 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 33.23 Å2
Baniso -1Baniso -2Baniso -3
1--6.4988 Å20 Å20 Å2
2--9.2391 Å20 Å2
3----2.7403 Å2
Refinement stepCycle: LAST / Resolution: 2→45.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4535 0 0 209 4744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054629
X-RAY DIFFRACTIONf_angle_d0.986212
X-RAY DIFFRACTIONf_dihedral_angle_d18.5441722
X-RAY DIFFRACTIONf_chiral_restr0.071681
X-RAY DIFFRACTIONf_plane_restr0.003786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04610.32451110.25052344X-RAY DIFFRACTION47
2.0461-2.09370.31021290.22872519X-RAY DIFFRACTION51
2.0937-2.14610.28481270.22692592X-RAY DIFFRACTION52
2.1461-2.20410.25371430.21572521X-RAY DIFFRACTION52
2.2041-2.26890.30771230.2332550X-RAY DIFFRACTION52
2.2689-2.34220.28721500.22142557X-RAY DIFFRACTION52
2.3422-2.42590.26521200.21052570X-RAY DIFFRACTION52
2.4259-2.5230.26961330.2112579X-RAY DIFFRACTION52
2.523-2.63780.25411530.22112559X-RAY DIFFRACTION52
2.6378-2.77690.26241390.22852597X-RAY DIFFRACTION53
2.7769-2.95080.31821450.22972575X-RAY DIFFRACTION53
2.9508-3.17860.2511280.22622610X-RAY DIFFRACTION53
3.1786-3.49840.25331430.21052616X-RAY DIFFRACTION53
3.4984-4.00440.23011510.20222623X-RAY DIFFRACTION53
4.0044-5.0440.24261290.18022673X-RAY DIFFRACTION54
5.044-45.88150.261590.22512775X-RAY DIFFRACTION57

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