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- PDB-8xov: The Crystal Structure of N-terminal kinase domain of human RSK-1 ... -

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Basic information

Entry
Database: PDB / ID: 8xov
TitleThe Crystal Structure of N-terminal kinase domain of human RSK-1 from Biortus.
ComponentsRibosomal protein S6 kinase alpha-1
KeywordsTRANSFERASE / 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 / ribosomal protein S6 kinase activity / CREB phosphorylation / hepatocyte proliferation / positive regulation of hepatic stellate cell activation / Gastrin-CREB signalling pathway via PKC and MAPK / RSK activation / negative regulation of TOR signaling / ERK/MAPK targets ...regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / ribosomal protein S6 kinase activity / CREB phosphorylation / hepatocyte proliferation / positive regulation of hepatic stellate cell activation / Gastrin-CREB signalling pathway via PKC and MAPK / RSK activation / negative regulation of TOR signaling / ERK/MAPK targets / Recycling pathway of L1 / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / protein serine/threonine/tyrosine kinase activity / positive regulation of cell differentiation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / chemical synaptic transmission / non-specific serine/threonine protein kinase / intracellular signal transduction / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / synapse / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / magnesium ion binding / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / cytoplasm / cytosol
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. / Protein kinase 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. / 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
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Ribosomal protein S6 kinase alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Zhang, B.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: To Be Published
Title: The Crystal Structure of N-terminal kinase domain of human RSK-1 from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Zhang, B.
History
DepositionJan 2, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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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)37,4705
Polymers36,7771
Non-polymers6924
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-3 kcal/mol
Surface area13080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.911, 54.346, 207.028
Angle α, β, γ (deg.)90.000, 94.075, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Ribosomal protein S6 kinase alpha-1 / S6K-alpha-1 / 90 kDa ribosomal protein S6 kinase 1 / p90-RSK 1 / p90RSK1 / p90S6K / MAP kinase- ...S6K-alpha-1 / 90 kDa ribosomal protein S6 kinase 1 / p90-RSK 1 / p90RSK1 / p90S6K / MAP kinase-activated protein kinase 1a / MAPK-activated protein kinase 1a / MAPKAP kinase 1a / MAPKAPK-1a / Ribosomal S6 kinase 1 / RSK-1


Mass: 36777.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KA1, MAPKAPK1A, RSK1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q15418, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M MgAC2, 0.1M Nacacodylate pH6.5, 15% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→33.7 Å / Num. obs: 11642 / % possible obs: 93.8 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 6
Reflection shellResolution: 2.55→2.66 Å / Rmerge(I) obs: 0.456 / Num. unique obs: 1470

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→33.7 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 14.433 / SU ML: 0.284 / Cross valid method: FREE R-VALUE / ESU R: 0.54 / ESU R Free: 0.299
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2517 606 5.206 %
Rwork0.2032 11035 -
all0.206 --
obs-11641 93.502 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 64.192 Å2
Baniso -1Baniso -2Baniso -3
1--5.626 Å2-0 Å2-0.381 Å2
2--9.58 Å20 Å2
3----3.86 Å2
Refinement stepCycle: LAST / Resolution: 2.55→33.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2113 0 43 51 2207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122205
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162076
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.6612966
X-RAY DIFFRACTIONr_angle_other_deg0.4961.5754832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3135257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.326514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.63510397
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.2591098
X-RAY DIFFRACTIONr_chiral_restr0.0660.2320
X-RAY DIFFRACTIONr_chiral_restr_other0.0810.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022411
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02450
X-RAY DIFFRACTIONr_nbd_refined0.2330.2402
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.21864
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21012
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21211
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.241
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1610.27
X-RAY DIFFRACTIONr_nbd_other0.180.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1750.23
X-RAY DIFFRACTIONr_mcbond_it6.0246.3461040
X-RAY DIFFRACTIONr_mcbond_other5.9936.3481040
X-RAY DIFFRACTIONr_mcangle_it9.249.4941293
X-RAY DIFFRACTIONr_mcangle_other9.2459.4971294
X-RAY DIFFRACTIONr_scbond_it6.5076.9691165
X-RAY DIFFRACTIONr_scbond_other6.5046.971166
X-RAY DIFFRACTIONr_scangle_it9.76110.2081673
X-RAY DIFFRACTIONr_scangle_other9.75910.2091674
X-RAY DIFFRACTIONr_lrange_it12.74375.3932335
X-RAY DIFFRACTIONr_lrange_other12.74474.892334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.6160.375520.363852X-RAY DIFFRACTION96.5812
2.616-2.6870.418400.343797X-RAY DIFFRACTION96.875
2.687-2.7640.325350.297783X-RAY DIFFRACTION96.5761
2.764-2.8490.282470.273748X-RAY DIFFRACTION95.3237
2.849-2.9420.319420.27728X-RAY DIFFRACTION96.01
2.942-3.0440.268370.288738X-RAY DIFFRACTION95.2088
3.044-3.1580.29290.22686X-RAY DIFFRACTION95.5882
3.158-3.2860.291360.198658X-RAY DIFFRACTION95.9889
3.286-3.430.19320.186638X-RAY DIFFRACTION94.2335
3.43-3.5960.295320.191598X-RAY DIFFRACTION94.5946
3.596-3.7880.211280.192581X-RAY DIFFRACTION92.4127
3.788-4.0150.192320.143517X-RAY DIFFRACTION92.5801
4.015-4.2880.159240.146506X-RAY DIFFRACTION91.6955
4.288-4.6250.209250.127457X-RAY DIFFRACTION91.1153
4.625-5.0570.215270.15414X-RAY DIFFRACTION88.5542
5.057-5.6380.3320.197361X-RAY DIFFRACTION87.9195
5.638-6.480.264220.208330X-RAY DIFFRACTION88.8889
6.48-7.8650.248180.218288X-RAY DIFFRACTION87.4286
7.865-10.8330.27490.173225X-RAY DIFFRACTION84.1727
10.833-33.70.2470.291130X-RAY DIFFRACTION79.6512

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