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- PDB-8eq5: Crystal structure of the N-terminal kinase domain of RSK2 in comp... -

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Basic information

Entry
Database: PDB / ID: 8eq5
TitleCrystal structure of the N-terminal kinase domain of RSK2 in complex with SPRED2 (131-160)
Components
  • Ribosomal protein S6 kinase alpha-3
  • Sprouty-related, EVH1 domain-containing protein 2
KeywordsTRANSFERASE / Kinase / SPRED / Complex / cell signaling / ERK/MEK pathway
Function / homology
Function and homology information


negative regulation of lens fiber cell differentiation / negative regulation of intracellular signal transduction / stem cell factor receptor binding / regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / FGFRL1 modulation of FGFR1 signaling / CREB phosphorylation / TORC1 signaling / Gastrin-CREB signalling pathway via PKC and MAPK / RSK activation ...negative regulation of lens fiber cell differentiation / negative regulation of intracellular signal transduction / stem cell factor receptor binding / regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / FGFRL1 modulation of FGFR1 signaling / CREB phosphorylation / TORC1 signaling / Gastrin-CREB signalling pathway via PKC and MAPK / RSK activation / protein serine/threonine kinase inhibitor activity / positive regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of epithelial to mesenchymal transition / toll-like receptor signaling pathway / transport vesicle membrane / ERK/MAPK targets / Recycling pathway of L1 / RAS signaling downstream of NF1 loss-of-function variants / negative regulation of MAPK cascade / central nervous system development / skeletal system development / positive regulation of cell differentiation / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of ERK1 and ERK2 cascade / Regulation of RAS by GAPs / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP) / chemical synaptic transmission / response to lipopolysaccharide / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / synapse / negative regulation of apoptotic process / protein kinase binding / nucleolus / magnesium ion binding / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
c-Kit-binding domain / SPRE, EVH1 domain / KBD domain profile. / Sprouty / Sprouty protein (Spry) / Sprouty (SPR) domain profile. / Ribosomal protein S6 kinase alpha-3, C-terminal catalytic domain / Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / WH1/EVH1 domain ...c-Kit-binding domain / SPRE, EVH1 domain / KBD domain profile. / Sprouty / Sprouty protein (Spry) / Sprouty (SPR) domain profile. / Ribosomal protein S6 kinase alpha-3, C-terminal catalytic domain / Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / 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. / PH-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-QCT / Ribosomal protein S6 kinase alpha-3 / Sprouty-related, EVH1 domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBonsor, D.A. / Lopez, J. / McCormick, F. / Simanshu, D.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)HHSN261200800001E United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: The ribosomal S6 kinase 2 (RSK2)-SPRED2 complex regulates the phosphorylation of RSK substrates and MAPK signaling.
Authors: Lopez, J. / Bonsor, D.A. / Sale, M.J. / Urisman, A. / Mehalko, J.L. / Cabanski-Dunning, M. / Castel, P. / Simanshu, D.K. / McCormick, F.
History
DepositionOct 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosomal protein S6 kinase alpha-3
B: Sprouty-related, EVH1 domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7643
Polymers38,3162
Non-polymers4481
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, 1:1 complex
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-2 kcal/mol
Surface area14460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.438, 41.105, 99.258
Angle α, β, γ (deg.)90.00, 113.87, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-605-

HOH

21A-628-

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 / 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: 35070.832 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 BL21(DE3) (bacteria)
References: UniProt: P51812, non-specific serine/threonine protein kinase
#2: Protein/peptide Sprouty-related, EVH1 domain-containing protein 2 / Spred-2


Mass: 3245.272 Da / Num. of mol.: 1 / Fragment: Residues 131-160 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q7Z698
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.03 Å3/Da / Density % sol: 39.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 30% w/v PEG 2K MME, 0.1 M Tris, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 16, 2022
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→49.39 Å / Num. obs: 28136 / % possible obs: 97.7 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.057 / Net I/σ(I): 8.8
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.771 / Num. unique obs: 1656 / CC1/2: 0.568 / Rpim(I) all: 0.752

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GUE

4gue


Resolution: 1.8→49.39 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 1440 5.12 %
Rwork0.183 --
obs0.185 28129 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.3 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 32 139 2499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.35741360.32172651X-RAY DIFFRACTION98
1.86-1.940.32011330.27032708X-RAY DIFFRACTION98
1.94-2.030.28991300.22142591X-RAY DIFFRACTION96
2.03-2.130.22551420.21232662X-RAY DIFFRACTION98
2.13-2.270.25221480.20332688X-RAY DIFFRACTION98
2.27-2.440.26981510.20042663X-RAY DIFFRACTION98
2.44-2.690.26611480.21692675X-RAY DIFFRACTION98
2.69-3.080.23321660.20092609X-RAY DIFFRACTION96
3.08-3.880.21021500.1672701X-RAY DIFFRACTION98
3.88-49.390.1731360.1422741X-RAY DIFFRACTION96
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)
11.40780.31070.03441.2740.30091.0705-0.0330.07510.0402-0.19130.0243-0.096-0.13440.10340.01650.2464-0.00890.02410.2201-0.01280.2253-5.53090.936934.462
22.6561-0.01980.82493.4526-0.19312.7337-0.0510.38060.1752-0.29610.19960.4237-0.165-0.2235-0.06870.8320.00460.03090.562-0.01780.8592-25.3914-0.116718.5564
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN 'A' AND RESID 49 THROUGH 346)
2X-RAY DIFFRACTION2(CHAIN 'B' AND RESID 141 THROUGH 146)

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