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- PDB-2z7r: Crystal Structure of the N-terminal Kinase Domain of Human RSK1 b... -

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Basic information

Entry
Database: PDB / ID: 2z7r
TitleCrystal Structure of the N-terminal Kinase Domain of Human RSK1 bound to Staurosporine
ComponentsRibosomal protein S6 kinase alpha-1Ribosome
KeywordsTRANSFERASE / protein kinase / cancer / kinase inhibitor / ATP-binding / Magnesium / Metal-binding / Nucleotide-binding / Phosphorylation / Polymorphism / Serine/threonine-protein kinase
Function / homology
Function and homology information


regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / positive regulation of hepatic stellate cell activation / ribosomal protein S6 kinase activity / hepatocyte proliferation / CREB phosphorylation / regulation of DNA-templated transcription in response to stress / negative regulation of TOR signaling / Gastrin-CREB signalling pathway via PKC and MAPK / RSK activation ...regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / positive regulation of hepatic stellate cell activation / ribosomal protein S6 kinase activity / hepatocyte proliferation / CREB phosphorylation / regulation of DNA-templated transcription in response to stress / negative regulation of TOR signaling / Gastrin-CREB signalling pathway via PKC and MAPK / RSK activation / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Recycling pathway of L1 / ERK/MAPK targets / protein serine/threonine/tyrosine kinase activity / positive regulation of cell differentiation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / chemical synaptic transmission / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / non-specific serine/threonine protein kinase / peptidyl-serine phosphorylation / intracellular signal transduction / cell cycle / protein serine kinase activity / synapse / protein serine/threonine kinase activity / negative regulation of apoptotic process / protein phosphorylation / positive regulation of DNA-templated transcription / magnesium ion binding / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal S6 kinase, N-terminal catalytic domain / 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. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 ...Ribosomal S6 kinase, N-terminal catalytic domain / 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. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Phosphorylase Kinase; domain 1 / 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
STAUROSPORINE / Ribosomal protein S6 kinase alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsIkuta, M. / Munshi, S.K.
CitationJournal: Protein Sci. / Year: 2007
Title: Crystal structures of the N-terminal kinase domain of human RSK1 bound to three different ligands: Implications for the design of RSK1 specific inhibitors.
Authors: Ikuta, M. / Kornienko, M. / Byrne, N. / Reid, J.C. / Mizuarai, S. / Kotani, H. / Munshi, S.K.
History
DepositionAug 28, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosomal protein S6 kinase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2442
Polymers36,7771
Non-polymers4671
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.261, 53.855, 119.978
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribosomal protein S6 kinase alpha-1 / Ribosome / S6K-alpha 1 / 90 kDa ribosomal protein S6 kinase 1 / p90-RSK 1 / Ribosomal S6 kinase 1 / RSK-1 / ...S6K-alpha 1 / 90 kDa ribosomal protein S6 kinase 1 / p90-RSK 1 / Ribosomal S6 kinase 1 / RSK-1 / pp90RSK1 / p90S6K / MAP kinase-activated protein kinase 1a / MAPKAPK1A


Mass: 36777.391 Da / Num. of mol.: 1 / Fragment: Residues 33-353
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KA1, RSK1 / Cell line (production host): SF21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q15418, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-STU / STAUROSPORINE / Staurosporine


Mass: 466.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.3 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12-16% PEG MME 2000, 150mM DL-malic acid, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 27, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 23744 / % possible obs: 98.6 % / Redundancy: 6 % / Biso Wilson estimate: 31.2 Å2

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Processing

Software
NameClassification
HKL-2000data collection
MOLREPphasing
CNXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VZO
Resolution: 2→20 Å
RfactorNum. reflection
Rfree0.286 1571
Rwork0.255 -
obs-21979
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2134 0 35 107 2276

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