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- PDB-5csj: S100B-RSK1 crystal structure B -

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Basic information

Entry
Database: PDB / ID: 5csj
TitleS100B-RSK1 crystal structure B
Components
  • Protein S100-B
  • Ribosomal protein S6 kinase alpha-1
KeywordsTRANSFERASE / Kinase / S100 / Inhibitor / Signaling
Function / homology
Function and homology information


negative regulation of skeletal muscle cell differentiation / regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / ribosomal protein S6 kinase activity / adaptive thermogenesis / hepatocyte proliferation / CREB phosphorylation / positive regulation of hepatic stellate cell activation / sympathetic neuron projection extension / RAGE receptor binding ...negative regulation of skeletal muscle cell differentiation / regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / ribosomal protein S6 kinase activity / adaptive thermogenesis / hepatocyte proliferation / CREB phosphorylation / positive regulation of hepatic stellate cell activation / sympathetic neuron projection extension / RAGE receptor binding / positive regulation of myelination / TORC1 signaling / Gastrin-CREB signalling pathway via PKC and MAPK / astrocyte differentiation / response to methylmercury / RSK activation / S100 protein binding / negative regulation of TOR signaling / response to anesthetic / ERK/MAPK targets / Recycling pathway of L1 / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / regulation of neuronal synaptic plasticity / Nuclear signaling by ERBB4 / ruffle / positive regulation of neuron differentiation / protein serine/threonine/tyrosine kinase activity / Transcriptional and post-translational regulation of MITF-M expression and activity / axonogenesis / response to glucocorticoid / central nervous system development / positive regulation of cell differentiation / TAK1-dependent IKK and NF-kappa-B activation / tau protein binding / memory / long-term synaptic potentiation / calcium-dependent protein binding / regulation of cell shape / microtubule cytoskeleton / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP) / cellular response to hypoxia / chemical synaptic transmission / learning or memory / protein phosphorylation / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / cell adhesion / cilium / ciliary basal body / positive regulation of apoptotic process / protein serine kinase activity / neuronal cell body / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / positive regulation of cell population proliferation / calcium ion binding / 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 / extracellular region / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Protein S100-B / Ribosomal S6 kinase, N-terminal catalytic domain / 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 domain / Protein kinase, C-terminal ...Protein S100-B / Ribosomal S6 kinase, N-terminal catalytic domain / 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 domain / 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: 2.7 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)26,6498
Polymers26,4533
Non-polymers1965
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-107 kcal/mol
Surface area10550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.960, 68.930, 91.490
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: 4434.127 Da / Num. of mol.: 1 / Fragment: UNP residues 696-735
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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.63 %
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: 2.7→38.12 Å / Num. obs: 7001 / % possible obs: 99.9 % / Redundancy: 12.3 % / Rsym value: 0.27 / Net I/σ(I): 9.19
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 13.08 % / Mean I/σ(I) obs: 2.19 / Num. unique all: 494 / Rsym value: 1.646 / % 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: 2.7→38.115 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2764 333 4.76 %
Rwork0.2034 --
obs0.2067 6998 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→38.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 5 14 1570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0221596
X-RAY DIFFRACTIONf_angle_d1.3762112
X-RAY DIFFRACTIONf_dihedral_angle_d14.085555
X-RAY DIFFRACTIONf_chiral_restr0.068239
X-RAY DIFFRACTIONf_plane_restr0.009278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7002-3.40170.32771640.25163254X-RAY DIFFRACTION100
3.4017-38.1190.2531690.18483411X-RAY DIFFRACTION100

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