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- PDB-8r58: The RSK 2 N-terminal kinase domain in complex with BMF (1-19) -

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Basic information

Entry
Database: PDB / ID: 8r58
TitleThe RSK 2 N-terminal kinase domain in complex with BMF (1-19)
Components
  • Bcl-2-modifying factor
  • Ribosomal protein S6 kinase alpha-3
KeywordsSIGNALING PROTEIN / RSK / Bcl-2-modifying factor / BMF / VF-motif / AGC kinase / Ribosomal s6 kinase
Function / homology
Function and homology information


regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / Activation of BMF and translocation to mitochondria / CREB phosphorylation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / TORC1 signaling / Gastrin-CREB signalling pathway via PKC and MAPK / RSK activation / anoikis / myosin complex ...regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / Activation of BMF and translocation to mitochondria / CREB phosphorylation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / TORC1 signaling / Gastrin-CREB signalling pathway via PKC and MAPK / RSK activation / anoikis / myosin complex / toll-like receptor signaling pathway / ERK/MAPK targets / positive regulation of release of cytochrome c from mitochondria / Recycling pathway of L1 / negative regulation of autophagy / central nervous system development / skeletal system development / positive regulation of cell differentiation / positive regulation of protein-containing complex assembly / cellular response to UV / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / chemical synaptic transmission / response to lipopolysaccharide / mitochondrial outer membrane / 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 / positive regulation of apoptotic process / 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
Bcl-2-modifying factor / Bcl-2-modifying factor, apoptosis / Ribosomal protein S6 kinase alpha-3, C-terminal catalytic domain / Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / 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. ...Bcl-2-modifying factor / Bcl-2-modifying factor, apoptosis / Ribosomal protein S6 kinase alpha-3, C-terminal catalytic domain / Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / 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. / 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
Similarity search - Domain/homology
Chem-QCT / Ribosomal protein S6 kinase alpha-3 / Bcl-2-modifying factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsSok, P. / Remenyi, A.
Funding support Hungary, 1items
OrganizationGrant numberCountry
Hungarian National Research, Development and Innovation OfficeKKP 126963 Hungary
CitationJournal: To Be Published
Title: A new kinase docking system for RSK AGC kinase domain
Authors: Alexa, A. / Sok, P. / Remenyi, A.
History
DepositionNov 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosomal protein S6 kinase alpha-3
B: Bcl-2-modifying factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1184
Polymers38,5772
Non-polymers5402
Water1086
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-2 kcal/mol
Surface area13450 Å2
Unit cell
Length a, b, c (Å)82.309, 88.256, 39.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-402-

GOL

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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: 36338.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal kinase domain of the Ribosomal s6 kinase 2
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 Bcl-2-modifying factor


Mass: 2239.344 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Peptide derived from the Bcl-2-modifying factor (1-19)
Source: (synth.) Homo sapiens (human) / References: UniProt: Q96LC9
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.85 Å3/Da / Density % sol: 33.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG 550, 0,1M Tris pH 8.5, 10% isopropanol, 1.25 M NaCl as reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.308→88.256 Å / Num. obs: 7716 / % possible obs: 89.6 % / Redundancy: 12.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.056 / Rrim(I) all: 0.215 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2% possible allRmerge(I) obs
2.308-2.49611.71.63870.36961.8
2.496-2.60812.81.8573860.477975.81.618
2.608-2.72112.872.3073860.720275.31.318
2.721-2.8312.653.1323860.830477.220.971
2.83-2.94212.723.3733860.884477.51
2.942-3.05812.213.4263850.915581.910.972
3.058-3.16913.343.6483870.922689.150.932

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
STARANISOdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→44.13 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.12 / Stereochemistry target values: ML
Details: Data was anisotropic, elipsoid truncation and anisotropic correction was used by STARANISO server
RfactorNum. reflection% reflection
Rfree0.2626 767 9.98 %
Rwork0.2349 --
obs0.2376 7685 58.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.31→44.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2320 0 38 6 2364
Refine LS restraintsType: f_plane_restr / Dev ideal: 0.006 / Number: 416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.490.3718350.3199322X-RAY DIFFRACTION14
2.49-2.740.3943890.3279771X-RAY DIFFRACTION34
2.74-3.130.34281270.29261218X-RAY DIFFRACTION52
3.13-3.940.26542400.23592129X-RAY DIFFRACTION90
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)
14.83641.155-0.50315.966-2.37839.4702-0.2010.9756-1.3612-0.78290.08140.84040.9314-0.08670.46070.40730.0629-0.02460.8386-0.08620.7967-28.23550.8611-12.0897
211.71350.38820.40714.32813.29588.5497-0.4363-0.4253-0.06410.12710.18050.2966-0.3232-0.00540.1710.35170.168-0.05640.39040.09380.1889-17.56437.4061-3.4714
36.6124-0.9038-1.90185.5090.05325.3359-0.3386-1.06421.44430.25650.5904-0.9586-0.35350.1742-0.15010.3370.0848-0.08180.5462-0.33370.4885-5.3516.7520.1773
45.5450.45790.86083.031-0.0810.1248-1.6711-1.26940.2188-2.11130.39670.6749-0.0434-0.0310.55041.09220.0562-0.01910.4377-0.3151.68934.369627.2875-4.3069
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 49 through 109 )
2X-RAY DIFFRACTION2chain 'A' and (resid 110 through 231 )
3X-RAY DIFFRACTION3chain 'A' and (resid 232 through 348 )
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 17 )

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