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- PDB-4gue: Structure of N-terminal kinase domain of RSK2 with flavonoid glyc... -

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Basic information

Entry
Database: PDB / ID: 4gue
TitleStructure of N-terminal kinase domain of RSK2 with flavonoid glycoside quercitrin
ComponentsRibosomal protein S6 kinase alpha-3
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Serine/threonine kinase domain / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / cytoplasm / cytosol
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
Chem-QCT / Ribosomal protein S6 kinase alpha-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsDerewenda, U. / Utepbergenov, D. / Szukalska, G. / Derewenda, Z.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Identification of quercitrin as an inhibitor of the p90 S6 ribosomal kinase (RSK): structure of its complex with the N-terminal domain of RSK2 at 1.8 A resolution.
Authors: Derewenda, U. / Artamonov, M. / Szukalska, G. / Utepbergenov, D. / Olekhnovich, N. / Parikh, H.I. / Kellogg, G.E. / Somlyo, A.V. / Derewenda, Z.S.
History
DepositionAug 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Sep 13, 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)35,6404
Polymers35,0711
Non-polymers5693
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.084, 40.686, 83.264
Angle α, β, γ (deg.)90.00, 114.31, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-403-

SO4

21A-516-

HOH

31A-626-

HOH

41A-756-

HOH

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Components

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


Mass: 35070.832 Da / Num. of mol.: 1 / Fragment: N-terminal kinase domain (UNP residues 45-346)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rps6ka3, Mapkapk1b, Rps6ka-rs1, Rsk2 / Production host: Escherichia coli (E. coli)
References: UniProt: P18654, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-QCT / 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxo-4H-chromen-3-yl 6-deoxy-alpha-L-mannopyranoside / quercitrin


Mass: 448.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20O11
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.16 Å3/Da / Density % sol: 43.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% Jeffamine ED2003, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 30, 2011
RadiationMonochromator: Double crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 29080 / Num. obs: 28004 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 4.3 % / Rsym value: 0.117 / Net I/σ(I): 15.2
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 4.65 / Rsym value: 0.303 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
PHENIX1.6.4_486refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3UBD

3ubd


Resolution: 1.8→25.293 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 20.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2047 1389 5.05 %
Rwork0.1712 --
obs0.1729 27492 97.72 %
all-28004 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.789 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.4085 Å20 Å2-3.8809 Å2
2--0.2734 Å20 Å2
3----5.682 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2255 0 38 260 2553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062356
X-RAY DIFFRACTIONf_angle_d0.9823190
X-RAY DIFFRACTIONf_dihedral_angle_d15.188869
X-RAY DIFFRACTIONf_chiral_restr0.066352
X-RAY DIFFRACTIONf_plane_restr0.004400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7997-1.86410.26421260.18992410X-RAY DIFFRACTION90
1.8641-1.93870.24821390.18082510X-RAY DIFFRACTION95
1.9387-2.02690.2031400.1792575X-RAY DIFFRACTION98
2.0269-2.13370.22811200.17122629X-RAY DIFFRACTION98
2.1337-2.26730.20141460.17062604X-RAY DIFFRACTION99
2.2673-2.44220.22761290.17762656X-RAY DIFFRACTION99
2.4422-2.68770.23271380.19092660X-RAY DIFFRACTION99
2.6877-3.07610.22531420.18162671X-RAY DIFFRACTION100
3.0761-3.87330.20431520.16272668X-RAY DIFFRACTION100
3.8733-25.29540.1761570.16182720X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.10410.338-0.50481.60720.1083.4198-0.15490.23810.207-0.13830.1006-0.0521-0.03170.20620.06410.2035-0.0899-0.03550.21280.04810.170438.16298.917414.336
22.08020.19170.44261.3852-0.1971.9468-0.17820.05360.173-0.17440.09850.22840.0669-0.19450.0690.1849-0.0666-0.03560.17530.00960.203419.56050.442725.0724
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 48:156) or (resseq 187:217))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 157:186) or (resseq 223:346))

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