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- PDB-8xey: The Crystal Structure of C-terminal kinase domain of RSK2 from Biortus -

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Basic information

Entry
Database: PDB / ID: 8xey
TitleThe Crystal Structure of C-terminal kinase domain of RSK2 from Biortus
ComponentsRibosomal protein S6 kinase alpha-3Ribosome
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 / Gastrin-CREB signalling pathway via PKC and MAPK / RSK activation / toll-like receptor signaling pathway / Recycling pathway of L1 / ERK/MAPK targets / cysteine-type endopeptidase inhibitor activity involved in apoptotic process ...regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / ribosomal protein S6 kinase activity / CREB phosphorylation / Gastrin-CREB signalling pathway via PKC and MAPK / RSK activation / toll-like receptor signaling pathway / Recycling pathway of L1 / ERK/MAPK targets / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / central nervous system development / skeletal system development / positive regulation of cell differentiation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Senescence-Associated Secretory Phenotype (SASP) / chemical synaptic transmission / positive regulation of cell growth / peptidyl-serine phosphorylation / response to lipopolysaccharide / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / synapse / nucleolus / negative regulation of apoptotic process / protein kinase binding / magnesium ion binding / signal transduction / 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. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...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. / 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
DI(HYDROXYETHYL)ETHER / Ribosomal protein S6 kinase alpha-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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 C-terminal kinase domain of RSK2 from Biortus
Authors: Wang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Zhang, B.
History
DepositionDec 13, 2023Deposition 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-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5163
Polymers38,3481
Non-polymers1682
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint0 kcal/mol
Surface area15730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.513, 46.513, 294.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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 / p90RSK3 / Insulin-stimulated ...S6K-alpha-3 / 90 kDa ribosomal protein S6 kinase 3 / p90-RSK 3 / p90RSK3 / Insulin-stimulated protein kinase 1 / ISPK-1 / MAP kinase-activated protein kinase 1b / MAPK-activated protein kinase 1b / MAPKAP kinase 1b / MAPKAPK-1b / Ribosomal S6 kinase 2 / RSK-2 / pp90RSK2


Mass: 38347.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KA3, ISPK1, MAPKAPK1B, RSK2 / Production host: Escherichia coli (E. coli)
References: UniProt: P51812, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH8.5, 25%PEG3,350

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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: Oct 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→49.01 Å / Num. obs: 10370 / % possible obs: 100 % / Redundancy: 14.8 % / Rmerge(I) obs: 0.174 / Net I/σ(I): 12.4
Reflection shellResolution: 2.65→2.78 Å / Rmerge(I) obs: 0.994 / Num. unique obs: 1336

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→45.984 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.901 / SU B: 14.576 / SU ML: 0.288 / Cross valid method: FREE R-VALUE / ESU R Free: 0.387
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2803 551 5.359 %
Rwork0.2016 9730 -
all0.206 --
obs-10281 99.971 %
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: 51.766 Å2
Baniso -1Baniso -2Baniso -3
1-3.143 Å2-0 Å2-0 Å2
2--3.143 Å2-0 Å2
3----6.285 Å2
Refinement stepCycle: LAST / Resolution: 2.65→45.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2480 0 11 58 2549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122544
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162324
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.6513445
X-RAY DIFFRACTIONr_angle_other_deg0.51.5675417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0825311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.837515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.74410435
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.35310119
X-RAY DIFFRACTIONr_chiral_restr0.0680.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022873
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02499
X-RAY DIFFRACTIONr_nbd_refined0.2250.2490
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.22182
X-RAY DIFFRACTIONr_nbtor_refined0.180.21253
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21382
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.257
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2120.220
X-RAY DIFFRACTIONr_nbd_other0.1740.2113
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1230.25
X-RAY DIFFRACTIONr_mcbond_it5.145.3541247
X-RAY DIFFRACTIONr_mcbond_other5.1385.3541247
X-RAY DIFFRACTIONr_mcangle_it7.9388.0061557
X-RAY DIFFRACTIONr_mcangle_other7.9358.011558
X-RAY DIFFRACTIONr_scbond_it4.8015.6351297
X-RAY DIFFRACTIONr_scbond_other4.7995.6351298
X-RAY DIFFRACTIONr_scangle_it7.458.3111888
X-RAY DIFFRACTIONr_scangle_other7.4488.3121889
X-RAY DIFFRACTIONr_lrange_it11.34364.6472788
X-RAY DIFFRACTIONr_lrange_other11.34764.6492785
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.65-2.7190.575410.3317000.3427420.8140.92699.86520.304
2.719-2.7930.445400.3126570.326970.9120.9321000.28
2.793-2.8740.289370.2626670.2647040.9290.9521000.229
2.874-2.9620.282310.246360.2426670.9260.9621000.212
2.962-3.0580.313220.2536420.2556640.9190.9581000.218
3.058-3.1650.243360.255980.256340.9350.9561000.21
3.165-3.2840.339340.2465940.2516290.9220.95699.8410.217
3.284-3.4170.27420.2275360.235780.9490.9661000.201
3.417-3.5680.315400.2085590.2155990.9380.9711000.186
3.568-3.7420.267250.2075040.2095290.9680.9741000.19
3.742-3.9420.268290.2135010.2165300.9530.9721000.2
3.942-4.180.214380.1824790.1845170.9650.9771000.169
4.18-4.4660.243290.1524330.1594620.9690.9851000.145
4.466-4.820.239180.1324310.1354490.9730.9881000.124
4.82-5.2740.272180.144070.1444250.9520.9881000.134
5.274-5.8870.256260.1553620.1613880.9620.9841000.145
5.887-6.7790.247170.1763300.183470.9670.9791000.165
6.779-8.2580.248160.182860.1843020.9730.9791000.176
8.258-11.4940.29690.1492450.1542540.9540.9841000.15
11.494-45.9840.34530.2671630.2691660.9260.951000.276

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