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- PDB-5csi: S100B-RSK1 crystal structure A' -

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Basic information

Entry
Database: PDB / ID: 5csi
TitleS100B-RSK1 crystal structure A'
Components
  • Protein S100-B
  • Ribosomal protein S6 kinase alpha-1
KeywordsTRANSFERASE / Kinase / Signaling / Inhibitor / S100
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 / Gastrin-CREB signalling pathway via PKC and MAPK / TORC1 signaling / response to methylmercury / RSK activation / astrocyte differentiation / 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: 2.13 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 ...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_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)27,4397
Polymers27,2793
Non-polymers1604
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-81 kcal/mol
Surface area9870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.310, 38.570, 173.410
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: 5260.097 Da / Num. of mol.: 1 / Fragment: UNP residues 689-735
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.: 40 / 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: 2.35 Å3/Da / Density % sol: 47.62 %
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: ID23-1 / Wavelength: 0.973 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 2.13→37.65 Å / Num. obs: 15160 / % possible obs: 99.9 % / Redundancy: 6.43 % / Rsym value: 0.055 / Net I/σ(I): 18.77
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 6.73 % / Mean I/σ(I) obs: 2.07 / Rsym value: 0.828 / % 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: 2.13→37.65 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 733 4.86 %
Rwork0.2048 --
obs0.2069 15085 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.13→37.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1508 0 4 40 1552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071546
X-RAY DIFFRACTIONf_angle_d0.932079
X-RAY DIFFRACTIONf_dihedral_angle_d15.378556
X-RAY DIFFRACTIONf_chiral_restr0.033235
X-RAY DIFFRACTIONf_plane_restr0.003274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1301-2.29460.34461540.2932764X-RAY DIFFRACTION100
2.2946-2.52550.28751370.21752828X-RAY DIFFRACTION100
2.5255-2.89080.24981450.2022839X-RAY DIFFRACTION100
2.8908-3.64160.25711430.22072884X-RAY DIFFRACTION100
3.6416-37.65580.22931540.18553037X-RAY DIFFRACTION100
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)
11.05820.25691.74241.91950.66014.4792-0.01810.65470.0173-0.5024-0.1197-0.2664-0.19331.31250.1860.45190.01590.09020.77030.04540.4412.4256-5.1003-19.1476
22.8294-0.64851.04092.6469-0.64232.42780.28390.68640.2321-1.3224-0.1082-0.4974-0.08180.8178-0.21261.00860.05490.20950.9287-0.05140.47918.7591-6.6178-35.9399
31.13960.96660.03442.6134-0.27642.80770.0140.5841-0.0729-0.54250.18810.56050.1911-0.3149-0.13711.11610.065-0.10280.84810.0320.532-0.0975-9.5839-35.3611
44.54520.1777-1.94015.215-1.59534.6905-0.1650.0824-0.3092-0.69720.41920.56240.28-0.4736-0.21540.5544-0.0107-0.05780.65470.05730.4114-1.0887-9.7484-22.7756
51.38910.6305-0.87541.0476-0.00593.99250.06260.1372-0.278-0.1810.024-0.00170.63590.5570.17540.47680.09630.00350.49060.05740.4765.4437-14.0845-14.5088
66.8849-0.64911.03355.5962-2.48156.48150.02310.31210.4688-0.2202-0.0539-0.06310.26310.24030.06280.32020.04160.01650.46470.05070.3461-5.5976-11.6109-2.2299
73.25690.9651-0.27750.71360.86493.1639-0.3362-0.525-0.20810.15090.29770.4280.07840.34990.08320.37170.0582-0.00050.31490.0340.44841.9231-3.0495-2.4162
87.01510.1467-0.98565.02630.03676.8511-0.1364-0.58261.71820.74720.1723-0.6017-1.15571.2002-0.31950.5415-0.0321-0.01830.5099-0.03710.60417.15884.2889-4.8667
92.57161.9308-0.20693.41550.22127.44070.7073-0.26551.8805-0.3658-0.2415-0.0555-1.0435-1.3620.0210.53760.17190.12980.57270.08440.8894-6.27574.4635-5.0387
103.8072-1.5271.15683.89781.52731.56450.60941.61830.4057-0.4768-0.27620.701-0.2234-1.0433-0.250.38130.10960.03390.86340.25510.6709-11.7229-4.4824-9.2239
116.45730.3854-2.0485.0082-0.28686.39760.13570.81880.762-0.40540.44410.2878-0.7595-0.2374-0.37860.4127-0.00750.00870.53030.13780.44692.1254-0.6245-17.4824
123.29061.6464-0.72341.851.92666.82510.31072.1893-0.9282-2.11280.60980.86420.4951-0.5776-0.7541.5882-0.2952-0.31111.30250.04041.0714-2.8367-20.01-28.5673
130.20630.23530.18132.0303-0.16432.25150.6189-1.11460.57810.1401-0.0967-0.15210.23610.689-0.3071.0672-0.16170.17370.93110.13821.367910.74267.806-11.1742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'E' and (resid -3 through 18 )
2X-RAY DIFFRACTION2chain 'E' and (resid 19 through 39 )
3X-RAY DIFFRACTION3chain 'E' and (resid 40 through 69 )
4X-RAY DIFFRACTION4chain 'E' and (resid 70 through 89 )
5X-RAY DIFFRACTION5chain 'F' and (resid -1 through 18 )
6X-RAY DIFFRACTION6chain 'F' and (resid 19 through 28 )
7X-RAY DIFFRACTION7chain 'F' and (resid 29 through 39 )
8X-RAY DIFFRACTION8chain 'F' and (resid 40 through 49 )
9X-RAY DIFFRACTION9chain 'F' and (resid 50 through 60 )
10X-RAY DIFFRACTION10chain 'F' and (resid 61 through 69 )
11X-RAY DIFFRACTION11chain 'F' and (resid 70 through 88 )
12X-RAY DIFFRACTION12chain 'C' and (resid 3 through 10 )
13X-RAY DIFFRACTION13chain 'B' and (resid 11 through 17 )

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