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- PDB-4l43: Crystal structures of human p70S6K1-T389A (form I) -

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Basic information

Entry
Database: PDB / ID: 4l43
TitleCrystal structures of human p70S6K1-T389A (form I)
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 / Resolution: 3 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
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)39,3242
Polymers38,9341
Non-polymers3901
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)79.572, 79.572, 112.749
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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: 38933.910 Da / Num. of mol.: 1 / Fragment: UNP residues 75-417 / Mutation: T389A
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

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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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.6M ammonium citrate, 0.1M Bis-Tris propane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9797 Å
DetectorType: CCD ADSC unsupported-q315 / Detector: CCD / Date: Mar 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionRedundancy: 6.9 % / Av σ(I) over netI: 18.51 / Number: 59631 / Rmerge(I) obs: 0.098 / Χ2: 1.08 / D res high: 3 Å / D res low: 50 Å / Num. obs: 8690 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.465099.410.0491.0236.4
5.136.4699.910.0620.8926.6
4.485.1310010.0811.1926.7
4.074.4899.910.1081.4826.9
3.784.0710010.1281.3866.9
3.563.7899.910.1611.2217
3.383.5610010.2180.9887
3.233.3810010.2750.8487
3.113.2310010.3810.8687.1
33.1110010.520.8477.1
ReflectionResolution: 3→50 Å / Num. obs: 8690 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3-3.117.10.521100
3.11-3.237.10.3811100
3.23-3.3870.2751100
3.38-3.5670.2181100
3.56-3.7870.161199.9
3.78-4.076.90.1281100
4.07-4.486.90.108199.9
4.48-5.136.70.0811100
5.13-6.466.60.062199.9
6.46-506.40.049199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 1 / SU B: 42.09 / SU ML: 0.334 / Cross valid method: THROUGHOUT / ESU R Free: 0.475 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2789 450 5.2 %RANDOM
Rwork0.22666 ---
obs0.22929 8160 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.167 Å2
Baniso -1Baniso -2Baniso -3
1-4.36 Å22.18 Å20 Å2
2--4.36 Å20 Å2
3----6.54 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 28 0 2526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222584
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0281.9843483
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9625313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53423.54113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.22815460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1461517
X-RAY DIFFRACTIONr_chiral_restr0.0690.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211935
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9051.51567
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.51922507
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.84631017
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8334.5976
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.18632584
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 36 -
Rwork0.309 574 -
obs--99.67 %
Refinement TLS params.Method: refined / Origin x: -39.788 Å / Origin y: 24.4082 Å / Origin z: -9.3852 Å
111213212223313233
T0.0794 Å2-0.0241 Å2-0.016 Å2-0.0664 Å2-0.0197 Å2--0.0046 Å2
L0.214 °2-0.101 °2-0.05 °2-1.2862 °2-0.6566 °2--0.6022 °2
S-0.021 Å °-0.0165 Å °0.0159 Å °-0.0218 Å °-0.0759 Å °-0.0825 Å °0.0951 Å °0.0209 Å °0.0969 Å °

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