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- PDB-5csn: S100B-RSK1 crystal structure C -

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Basic information

Entry
Database: PDB / ID: 5csn
TitleS100B-RSK1 crystal structure C
Components
  • Protein S100-B
  • Ribosomal protein S6 kinase alpha-1
KeywordsTRANSFERASE / S100 / Kinase / Signaling / Inhibitor
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 / adaptive thermogenesis / CREB phosphorylation / hepatocyte proliferation / positive regulation of hepatic stellate cell activation / sympathetic neuron projection extension / RAGE receptor binding / Gastrin-CREB signalling pathway via PKC and MAPK ...regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / ribosomal protein S6 kinase activity / adaptive thermogenesis / CREB phosphorylation / hepatocyte proliferation / positive regulation of hepatic stellate cell activation / sympathetic neuron projection extension / RAGE receptor binding / Gastrin-CREB signalling pathway via PKC and MAPK / RSK activation / negative regulation of TOR signaling / S100 protein binding / ERK/MAPK targets / Recycling pathway of L1 / regulation of neuronal synaptic plasticity / TRAF6 mediated NF-kB activation / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Advanced glycosylation endproduct receptor signaling / Transcriptional and post-translational regulation of MITF-M expression and activity / Nuclear signaling by ERBB4 / ruffle / protein serine/threonine/tyrosine kinase activity / positive regulation of neuron differentiation / : / axonogenesis / central nervous system development / positive regulation of cell differentiation / TAK1-dependent IKK and NF-kappa-B activation / tau protein binding / memory / calcium-dependent protein binding / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / chemical synaptic transmission / positive regulation of canonical NF-kappaB signal transduction / learning or memory / non-specific serine/threonine protein kinase / cell adhesion / intracellular signal transduction / protein phosphorylation / intracellular membrane-bounded organelle / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / calcium ion binding / positive regulation of cell population proliferation / synapse / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / magnesium ion binding / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / zinc ion binding / extracellular region / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal S6 kinase, N-terminal catalytic domain / Protein S100-B / Ribosomal protein S6 kinase II / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand / Protein kinase, C-terminal ...Ribosomal S6 kinase, N-terminal catalytic domain / Protein S100-B / Ribosomal protein S6 kinase II / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand / 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. / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / 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
Protein S100-B / Ribosomal protein S6 kinase alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsGogl, G. / Nyitray, L.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis of Ribosomal S6 Kinase 1 (RSK1) Inhibition by S100B Protein: MODULATION OF THE EXTRACELLULAR SIGNAL-REGULATED KINASE (ERK) SIGNALING CASCADE IN A CALCIUM-DEPENDENT WAY.
Authors: Gogl, G. / Alexa, A. / Kiss, B. / Katona, G. / Kovacs, M. / Bodor, A. / Remenyi, A. / Nyitray, L.
History
DepositionJul 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein S100-B
B: Protein S100-B
C: Ribosomal protein S6 kinase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3837
Polymers26,2223
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-67 kcal/mol
Surface area10740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.790, 39.930, 178.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein S100-B / S-100 protein beta chain / S-100 protein subunit beta / S100 calcium-binding protein B


Mass: 11009.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100B / Production host: Escherichia coli (E. coli) / References: UniProt: P04271
#2: Protein/peptide Ribosomal protein S6 kinase alpha-1 / S6K-alpha-1 / 90 kDa ribosomal protein S6 kinase 1 / p90S6K / MAP kinase-activated protein kinase ...S6K-alpha-1 / 90 kDa ribosomal protein S6 kinase 1 / p90S6K / MAP kinase-activated protein kinase 1a / MAPKAPK-1a / Ribosomal S6 kinase 1 / RSK-1


Mass: 4203.685 Da / Num. of mol.: 1 / Fragment: UNP residues 683-720
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KA1, MAPKAPK1A, RSK1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q15418, non-specific serine/threonine protein kinase
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Hepes 7, 150 mM NaCl, 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.95→44.59 Å / Num. obs: 6056 / % possible obs: 99.9 % / Redundancy: 17.32 % / Rsym value: 0.155 / Net I/σ(I): 15.85
Reflection shellResolution: 2.95→3.03 Å / Redundancy: 17.81 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 444 / Rsym value: 2.126 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1750refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CZT

3czt


Resolution: 2.95→44.585 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2785 280 4.66 %
Rwork0.2514 --
obs0.2526 6014 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→44.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1572 0 4 0 1576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111622
X-RAY DIFFRACTIONf_angle_d0.8492149
X-RAY DIFFRACTIONf_dihedral_angle_d15.005570
X-RAY DIFFRACTIONf_chiral_restr0.033241
X-RAY DIFFRACTIONf_plane_restr0.003283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.71640.35161430.29152794X-RAY DIFFRACTION100
3.7164-44.59010.25211370.23812940X-RAY DIFFRACTION100

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