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- PDB-3g51: Structural diversity of the active conformation of the N-terminal... -

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Basic information

Entry
Database: PDB / ID: 3g51
TitleStructural diversity of the active conformation of the N-terminal kinase domain of p90 ribosomal S6 kinase 2
ComponentsRibosomal protein S6 kinase alpha-3Ribosome
KeywordsTRANSFERASE / N-terminal kinase domain of p90 ribosomal S6 kinase 2 / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase
Function / homology
Function and homology information


RSK activation / CREB phosphorylation / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / Gastrin-CREB signalling pathway via PKC and MAPK / Senescence-Associated Secretory Phenotype (SASP) / ribosomal protein S6 kinase activity / ERK/MAPK targets / toll-like receptor signaling pathway / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to lipopolysaccharide ...RSK activation / CREB phosphorylation / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / Gastrin-CREB signalling pathway via PKC and MAPK / Senescence-Associated Secretory Phenotype (SASP) / ribosomal protein S6 kinase activity / ERK/MAPK targets / toll-like receptor signaling pathway / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to lipopolysaccharide / non-specific serine/threonine protein kinase / intracellular signal transduction / cell cycle / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / protein kinase binding / magnesium ion binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S6 kinase alpha-3, C-terminal catalytic domain / 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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...Ribosomal protein S6 kinase alpha-3, C-terminal catalytic domain / 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. / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Ribosomal protein S6 kinase alpha-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKurinov, I.
CitationJournal: Plos One / Year: 2009
Title: Structural diversity of the active N-terminal kinase domain of p90 ribosomal S6 kinase 2
Authors: Malakhova, M. / Kurinov, I. / Liu, K. / Zheng, D. / D'Angelo, I. / Shim, J.H. / Steinman, V. / Bode, A.M. / Dong, Z.
History
DepositionFeb 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosomal protein S6 kinase alpha-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9822
Polymers37,4751
Non-polymers5061
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.167, 51.381, 140.873
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-3 / Ribosome / S6K-alpha 3 / 90 kDa ribosomal protein S6 kinase 3 / p90-RSK 3 / Ribosomal S6 kinase 2 / RSK-2 / ...S6K-alpha 3 / 90 kDa ribosomal protein S6 kinase 3 / p90-RSK 3 / Ribosomal S6 kinase 2 / RSK-2 / pp90RSK2 / MAP kinase-activated protein kinase 1b / MAPKAPK1B


Mass: 37475.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Gene: Mus musculus ribosomal protein S6 kinase 2, Rps6ka-rs1, Rps6ka3, Rsk2
Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codon Plus (DE3)-RILP
References: UniProt: P18654, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: The diluted protein at different concentrations (2.5 mg/ml 10 mg/ml) was mixed at a 2:1 ratio with precipitant solution (6%-10% PEG 3350, 0.2 M proline, 0.1 M Hepes pH 7.5). , VAPOR ...Details: The diluted protein at different concentrations (2.5 mg/ml 10 mg/ml) was mixed at a 2:1 ratio with precipitant solution (6%-10% PEG 3350, 0.2 M proline, 0.1 M Hepes pH 7.5). , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2008 / Details: HFM, VFM, microdiffractometer
RadiationMonochromator: Si 111 Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→36 Å / Num. all: 35155 / Num. obs: 35092 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.091
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5 % / % possible all: 94.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VZO

1vzo


Resolution: 1.8→36.3 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1637 -RANDOM
Rwork0.204 ---
all0.216 35245 --
obs0.216 32826 93 %-
Refinement stepCycle: LAST / Resolution: 1.8→36.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 31 274 2575
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_deg0.6
X-RAY DIFFRACTIONf_improper_angle_d0.05

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