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- PDB-1vzo: The structure of the N-terminal kinase domain of MSK1 reveals a n... -

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Basic information

Entry
Database: PDB / ID: 1vzo
TitleThe structure of the N-terminal kinase domain of MSK1 reveals a novel autoinhibitory conformation for a dual kinase protein
ComponentsRIBOSOMAL PROTEIN S6 KINASE ALPHA 5
KeywordsTRANSFERASE / PROTEIN KINASE / PHOSPHORYLATION / SERINE/THREONINE PROTEIN KINASE
Function / homology
Function and homology information


positive regulation of CREB transcription factor activity / CREB phosphorylation / TORC1 signaling / regulation of postsynapse organization / interleukin-1-mediated signaling pathway / negative regulation of cytokine production / ERK/MAPK targets / Recycling pathway of L1 / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling ...positive regulation of CREB transcription factor activity / CREB phosphorylation / TORC1 signaling / regulation of postsynapse organization / interleukin-1-mediated signaling pathway / negative regulation of cytokine production / 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 / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / inflammatory response / 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. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Ribosomal protein S6 kinase alpha-5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSmith, K.J. / Carter, P.S. / Bridges, A. / Horrocks, P. / Lewis, C. / Pettman, G. / Clarke, A. / Brown, M. / Hughes, J. / Wilkinson, M. ...Smith, K.J. / Carter, P.S. / Bridges, A. / Horrocks, P. / Lewis, C. / Pettman, G. / Clarke, A. / Brown, M. / Hughes, J. / Wilkinson, M. / Bax, B. / Reith, A.
CitationJournal: Structure / Year: 2004
Title: The Structure of Msk1 Reveals a Novel Autoinhibitory Conformation for a Dual Kinase Protein
Authors: Smith, K.J. / Carter, P.S. / Bridges, A. / Horrocks, P. / Lewis, C. / Pettman, G. / Clarke, A. / Brown, M. / Hughes, J. / Wilkinson, M. / Bax, B. / Reith, A.
History
DepositionMay 21, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBOSOMAL PROTEIN S6 KINASE ALPHA 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0893
Polymers39,9141
Non-polymers1742
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.629, 73.772, 89.118
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 KINASE-1 / MSK1 / RSK-LIKE PROTEIN KINASE / 90 KDA RIBOSOMAL ...NUCLEAR MITOGEN-AND-STRESS-ACTIVATED KINASE-1 / MSK1 / RSK-LIKE PROTEIN KINASE / 90 KDA RIBOSOMAL PROTEIN S6 KINASE 5 / RLSK


Mass: 39914.375 Da / Num. of mol.: 1 / Fragment: N-TERMINAL KINASE DOMAIN, RESIDUES 1-350 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: A COVALENT B-MERCAPTOETHANOL ADDUCT INCLUDED ON CYSTINE A 304
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: BACMID / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O75582, EC: 2.7.1.37
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSERINE/THREONINE KINASE THAT MAY PLAY A ROLE IN MEDIATING THE GROWTH-FACTOR AND STRESS INDUCED ...SERINE/THREONINE KINASE THAT MAY PLAY A ROLE IN MEDIATING THE GROWTH-FACTOR AND STRESS INDUCED ACTIVATION OF THE TRANSCRIPTION FACTOR CREB. ESSENTIAL ROLE IN THE CONTROL OF RELA TRANSCRIPTIONAL ACTIVITY IN RESPONSE TO TNF. ENGINEERED MUTATION SER 212 ASP, CHAIN A
Sequence detailsSERINE 212 MUTATED TO ASPARTIC ACID

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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: 2.74 Å3/Da / Density % sol: 55.17 %
Description: SOME DATA WERE EXCLUDED BECAUSE OF ICE-RINGS WHICH AFFECTED REFINEMENT
Crystal growpH: 9.5 / Details: 2.0M AMMONIUM SULPHATE, 0.1M TRIS PH8.5, pH 9.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9326
DetectorDate: Jun 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9326 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 34183 / % possible obs: 94.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.6
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 4.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ATP

1atp


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.01 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3400 10 %RANDOM
Rwork0.208 ---
obs-30768 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 29.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20 Å2
2--0.5 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2532 0 9 182 2723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212632
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9653556
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.515324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021934
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21073
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2178
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.29731609
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.97362594
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.54661023
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.9338962
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.286 291
Rwork0.238 2624

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