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- PDB-4l46: Crystal structures of human p70S6K1-WT -

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Basic information

Entry
Database: PDB / ID: 4l46
TitleCrystal structures of human p70S6K1-WT
ComponentsRPS6KB1 proteinP70-S6 Kinase 1
KeywordsTRANSFERASE / Protein kinase
Function / homology
Function and homology information


long-chain fatty acid import into cell / response to electrical stimulus involved in regulation of muscle adaptation / skeletal muscle atrophy / positive regulation of skeletal muscle tissue growth / regulation of glucose import / ribosomal protein S6 kinase activity / response to L-leucine / cellular response to nutrient / phosphatidylinositol-mediated signaling / response to glucagon ...long-chain fatty acid import into cell / response to electrical stimulus involved in regulation of muscle adaptation / skeletal muscle atrophy / positive regulation of skeletal muscle tissue growth / regulation of glucose import / ribosomal protein S6 kinase activity / response to L-leucine / cellular response to nutrient / phosphatidylinositol-mediated signaling / response to glucagon / response to testosterone / positive regulation of smooth muscle cell migration / TOR signaling / mTORC1-mediated signalling / germ cell development / positive regulation of translational initiation / skeletal muscle contraction / long-term memory / behavioral fear response / response to tumor necrosis factor / response to glucose / response to mechanical stimulus / negative regulation of insulin receptor signaling pathway / positive regulation of TORC1 signaling / protein serine/threonine/tyrosine kinase activity / cellular response to dexamethasone stimulus / positive regulation of mitotic cell cycle / response to nutrient levels / positive regulation of translation / protein phosphatase 2A binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / PDZ domain binding / negative regulation of extrinsic apoptotic signaling pathway / peptide binding / positive regulation of smooth muscle cell proliferation / G1/S transition of mitotic cell cycle / modulation of chemical synaptic transmission / response to toxic substance / cellular response to growth factor stimulus / cellular response to type II interferon / cellular response to insulin stimulus / cell migration / postsynapse / peptidyl-serine phosphorylation / response to ethanol / mitochondrial outer membrane / response to lipopolysaccharide / non-specific serine/threonine protein kinase / neuron projection / protein kinase activity / response to xenobiotic stimulus / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / signal transduction / mitochondrion / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S6 kinase / 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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...Ribosomal protein S6 kinase / 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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-5FI / Ribosomal protein S6 kinase beta-1 / Ribosomal protein S6 kinase beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.01 Å
AuthorsWang, J. / Zhong, C. / Ding, J.
CitationJournal: Biochem.J. / Year: 2013
Title: Crystal structures of S6K1 provide insights into the regulation mechanism of S6K1 by the hydrophobic motif
Authors: Wang, J. / Zhong, C. / Wang, F. / Qu, F. / Ding, J.
History
DepositionJun 7, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RPS6KB1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5964
Polymers39,0441
Non-polymers5523
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.139, 81.139, 111.047
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Detailsbiological unit is monomer

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Components

#1: Protein RPS6KB1 protein / P70-S6 Kinase 1 / Ribosomal protein S6 kinase beta-1 / Ribosomal protein S6 kinase / 70kDa / polypeptide 1 / isoform CRA_c


Mass: 39043.914 Da / Num. of mol.: 1 / Fragment: UNP residues 75-417
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KB1, hCG_1815774 / Plasmid: pFastBacHTB / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Spodoptera frugiperda / References: UniProt: Q7Z721, UniProt: P23443*PLUS
#2: Chemical ChemComp-5FI / 2-{[4-(5-ethylpyrimidin-4-yl)piperazin-1-yl]methyl}-5-(trifluoromethyl)-1H-benzimidazole


Mass: 390.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21F3N6
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 2.7 Å3/Da / Density % sol: 54.49 % / Mosaicity: 0.379 °
Crystal growTemperature: 289 K / Method: hanging drop / pH: 6.8
Details: 2.2M ammonium sulfate, 0.01M magnesium chloride, 0.1M HEPES, pH 6.8, hanging drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: CCD ADSC unsupported-q315 / Detector: CCD / Date: Nov 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionRedundancy: 7.1 % / Av σ(I) over netI: 21.33 / Number: 62775 / Rmerge(I) obs: 0.092 / Χ2: 1.1 / D res high: 3 Å / D res low: 50 Å / Num. obs: 8815 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.465099.610.0530.9586.6
5.136.4610010.0761.2716.8
4.485.1310010.0911.4587.1
4.074.4810010.0931.4087.1
3.784.0710010.0940.9827.2
3.563.7810010.1191.1827.2
3.383.5610010.1751.0357.3
3.233.3810010.2610.9047.3
3.113.2310010.3940.9057.3
33.1110010.5490.8587.3
ReflectionResolution: 3→50 Å / Num. obs: 8815 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.092 / Χ2: 1.095 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3-3.117.30.5498530.8581100
3.11-3.237.30.3948540.9051100
3.23-3.387.30.2618760.9041100
3.38-3.567.30.1758551.0351100
3.56-3.787.20.1198711.1821100
3.78-4.077.20.0948780.9821100
4.07-4.487.10.0938741.4081100
4.48-5.137.10.0918941.4581100
5.13-6.466.80.0768961.2711100
6.46-506.60.0539640.958199.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.01→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 1 / SU B: 62.274 / SU ML: 0.488 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.456 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2686 456 5.2 %RANDOM
Rwork0.2173 ---
obs0.22 8793 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 128.5 Å2 / Biso mean: 53.4586 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å20.75 Å20 Å2
2--1.51 Å20 Å2
3----2.26 Å2
Refinement stepCycle: LAST / Resolution: 3.01→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 34 0 2582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222629
X-RAY DIFFRACTIONr_angle_refined_deg1.9161.9893544
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6345314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.21823.391115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.16615469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1021517
X-RAY DIFFRACTIONr_chiral_restr0.1230.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211954
X-RAY DIFFRACTIONr_mcbond_it0.781.51576
X-RAY DIFFRACTIONr_mcangle_it1.36922527
X-RAY DIFFRACTIONr_scbond_it2.79631053
X-RAY DIFFRACTIONr_scangle_it3.854.51017
X-RAY DIFFRACTIONr_rigid_bond_restr1.9732629
LS refinement shellResolution: 3.01→3.083 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 30 -
Rwork0.333 584 -
all-614 -
obs--99.51 %
Refinement TLS params.Method: refined / Origin x: 42.3473 Å / Origin y: -23.6024 Å / Origin z: 9.02 Å
111213212223313233
T0.4563 Å20.0658 Å2-0.2728 Å2-0.1656 Å2-0.0434 Å2--0.2083 Å2
L2.3415 °21.3533 °2-1.1729 °2-2.7801 °2-2.1215 °2--3.6332 °2
S-0.0425 Å °-0.0472 Å °0.0448 Å °-0.3763 Å °0.2792 Å °0.0256 Å °0.5933 Å °-0.01 Å °-0.2368 Å °

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