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- PDB-5csf: S100B-RSK1 crystal structure A -

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Basic information

Entry
Database: PDB / ID: 5csf
TitleS100B-RSK1 crystal structure A
Components
  • Protein S100-B
  • Ribosomal protein S6 kinase alpha-1
KeywordsTRANSFERASE / Complex / 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 / positive regulation of hepatic stellate cell activation / adaptive thermogenesis / hepatocyte proliferation / CREB phosphorylation / sympathetic neuron projection extension / RAGE receptor binding / TORC1 signaling / 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 / positive regulation of hepatic stellate cell activation / adaptive thermogenesis / hepatocyte proliferation / CREB phosphorylation / sympathetic neuron projection extension / RAGE receptor binding / TORC1 signaling / Gastrin-CREB signalling pathway via PKC and MAPK / RSK activation / S100 protein binding / negative regulation of TOR signaling / ERK/MAPK targets / Recycling pathway of L1 / TRAF6 mediated NF-kB activation / regulation of neuronal synaptic plasticity / Advanced glycosylation endproduct receptor signaling / Nuclear signaling by ERBB4 / ruffle / Transcriptional and post-translational regulation of MITF-M expression and activity / 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 / microtubule cytoskeleton / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP) / chemical synaptic transmission / cilium / ciliary basal body / positive regulation of canonical NF-kappaB signal transduction / eukaryotic translation initiation factor 2alpha kinase activity / learning or memory / 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 / cell adhesion / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / intracellular membrane-bounded organelle / neuronal cell body / positive regulation of cell population proliferation / synapse / calcium ion binding / 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
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 / Resolution: 2.4 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 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)28,1217
Polymers27,9603
Non-polymers1604
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-95 kcal/mol
Surface area10410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.300, 39.240, 172.820
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 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: 5941.814 Da / Num. of mol.: 1 / Fragment: UNP residues 683-735
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
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: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→43.205 Å / Num. obs: 10773 / % possible obs: 99.1 % / Redundancy: 4.34 % / Rsym value: 0.034 / Net I/σ(I): 18.67
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.06 / Num. unique all: 774 / Rsym value: 0.546 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIXdev_1750refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 2.4→43.205 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2907 530 4.95 %
Rwork0.2432 --
obs0.2455 10708 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→43.205 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 4 4 1512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091524
X-RAY DIFFRACTIONf_angle_d1.2452048
X-RAY DIFFRACTIONf_dihedral_angle_d14.853542
X-RAY DIFFRACTIONf_chiral_restr0.055233
X-RAY DIFFRACTIONf_plane_restr0.008269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.64160.36291430.29682453X-RAY DIFFRACTION99
2.6416-3.02370.29421210.27342527X-RAY DIFFRACTION99
3.0237-3.80920.31931210.2712534X-RAY DIFFRACTION99
3.8092-43.2120.2681450.21762664X-RAY DIFFRACTION98

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