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- PDB-8wf4: The Crystal Structure of RSK1 from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8wf4
TitleThe Crystal Structure of RSK1 from Biortus.
ComponentsRibosomal protein S6 kinase alpha-1
KeywordsTRANSFERASE / Kinase / Serine / threonine-protein kinase / Cell cycle / Host-virus interaction / Stress response / ATP-binding / Magnesium / Metal-binding / Nucleotide-binding
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
Ribosomal protein S6 kinase alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Qi, J. / Li, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of RSK1 from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Qi, J. / Li, J.
History
DepositionSep 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: 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
B: Ribosomal protein S6 kinase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2886
Polymers73,0402
Non-polymers2484
Water1,29772
1
A: Ribosomal protein S6 kinase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6443
Polymers36,5201
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosomal protein S6 kinase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6443
Polymers36,5201
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.676, 143.632, 60.228
Angle α, β, γ (deg.)90.000, 95.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribosomal protein S6 kinase alpha-1


Mass: 36519.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KA1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15418
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Hepes pH7.0, 15% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.953719 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953719 Å / Relative weight: 1
ReflectionResolution: 2.65→47.88 Å / Num. obs: 19469 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9
Reflection shellResolution: 2.65→2.78 Å / Rmerge(I) obs: 0.888 / Num. unique obs: 2577

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→46.049 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.898 / SU B: 36.517 / SU ML: 0.6 / Cross valid method: FREE R-VALUE / ESU R Free: 0.418
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.309 948 4.876 %
Rwork0.239 18494 -
all0.242 --
obs-19442 99.846 %
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: 70 Å2
Baniso -1Baniso -2Baniso -3
1--9.519 Å20 Å2-0.933 Å2
2---5.541 Å20 Å2
3---14.938 Å2
Refinement stepCycle: LAST / Resolution: 2.65→46.049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4559 0 16 72 4647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0124663
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164303
X-RAY DIFFRACTIONr_angle_refined_deg0.6371.6566295
X-RAY DIFFRACTIONr_angle_other_deg0.2311.5710061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6645574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.659524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.29210837
X-RAY DIFFRACTIONr_dihedral_angle_6_deg9.43710206
X-RAY DIFFRACTIONr_chiral_restr0.0320.2704
X-RAY DIFFRACTIONr_chiral_restr_other0.030.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025206
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02874
X-RAY DIFFRACTIONr_nbd_refined0.1710.2886
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.24225
X-RAY DIFFRACTIONr_nbtor_refined0.1640.22300
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.22436
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2107
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0460.27
X-RAY DIFFRACTIONr_nbd_other0.1060.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1150.28
X-RAY DIFFRACTIONr_mcbond_it1.768.2732308
X-RAY DIFFRACTIONr_mcbond_other1.7598.2732308
X-RAY DIFFRACTIONr_mcangle_it3.12212.3972878
X-RAY DIFFRACTIONr_mcangle_other3.12112.3982879
X-RAY DIFFRACTIONr_scbond_it1.3318.4122355
X-RAY DIFFRACTIONr_scbond_other1.3318.4112356
X-RAY DIFFRACTIONr_scangle_it2.4512.5433417
X-RAY DIFFRACTIONr_scangle_other2.4512.5433418
X-RAY DIFFRACTIONr_lrange_it5.545101.9395099
X-RAY DIFFRACTIONr_lrange_other5.54101.9515098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.7190.396660.3961342X-RAY DIFFRACTION99.929
2.719-2.7930.464790.4161331X-RAY DIFFRACTION99.6466
2.793-2.8730.314640.3141304X-RAY DIFFRACTION99.854
2.873-2.9620.344620.3441232X-RAY DIFFRACTION99.8457
2.962-3.0580.406690.3611235X-RAY DIFFRACTION99.9234
3.058-3.1650.337640.3371149X-RAY DIFFRACTION99.3448
3.165-3.2840.367590.2771136X-RAY DIFFRACTION99.8329
3.284-3.4170.294500.2751078X-RAY DIFFRACTION99.9114
3.417-3.5680.328480.2461074X-RAY DIFFRACTION99.9109
3.568-3.7410.353510.221995X-RAY DIFFRACTION100
3.741-3.9420.302480.202966X-RAY DIFFRACTION100
3.942-4.180.28450.189885X-RAY DIFFRACTION100
4.18-4.4660.215470.16861X-RAY DIFFRACTION100
4.466-4.820.199380.154786X-RAY DIFFRACTION99.8788
4.82-5.2740.346450.175731X-RAY DIFFRACTION100
5.274-5.8870.283320.216667X-RAY DIFFRACTION99.8571
5.887-6.7790.333330.244595X-RAY DIFFRACTION99.841
6.779-8.2580.353280.189489X-RAY DIFFRACTION100
8.258-11.4950.2110.141398X-RAY DIFFRACTION100
11.495-46.0490.18390.183240X-RAY DIFFRACTION99.6

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