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- PDB-4l44: Crystal structures of human p70S6K1-T389A (form II) -

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Basic information

Entry
Database: PDB / ID: 4l44
TitleCrystal structures of human p70S6K1-T389A (form II)
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: 2.9 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: RPS6KB1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6786
Polymers38,9341
Non-polymers7445
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)77.961, 77.961, 113.829
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: 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
#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: 2.56 Å3/Da / Density % sol: 52.04 % / Mosaicity: 0.564 °
Crystal growTemperature: 289 K / Method: hanging drop / pH: 7.2
Details: 2M lithium sulfate, 0.05M magnesium sulfate, 0.05M HEPES, pH 7.2, 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: Feb 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionRedundancy: 3.9 % / Av σ(I) over netI: 12.85 / Number: 37254 / Rmerge(I) obs: 0.134 / Χ2: 1.51 / D res high: 2.9 Å / D res low: 50 Å / Num. obs: 9546 / % possible obs: 98.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.245097.510.0931.9363.6
4.966.2498.610.0961.723.7
4.334.9697.310.1032.053.7
3.944.339810.111.8163.8
3.653.9498.510.1351.7533.9
3.443.6599.410.1621.5594
3.273.4499.910.1931.3264.1
3.123.2799.910.2371.1544.1
33.1210010.2931.0394.1
2.9399.710.3760.9314.1
ReflectionResolution: 2.9→50 Å / Num. obs: 9546 / % possible obs: 98.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.134 / Χ2: 1.513 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-34.10.3769320.931199.7
3-3.124.10.2939411.0391100
3.12-3.274.10.2379571.154199.9
3.27-3.444.10.1939511.326199.9
3.44-3.6540.1629331.559199.4
3.65-3.943.90.1359481.753198.5
3.94-4.333.80.119411.816198
4.33-4.963.70.1039562.05197.3
4.96-6.243.70.0969541.72198.6
6.24-503.60.09310331.936197.5

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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: 2.9→50 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.834 / Occupancy max: 1 / Occupancy min: 1 / SU B: 42.571 / SU ML: 0.361 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.485 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2978 475 5.2 %RANDOM
Rwork0.2432 ---
obs0.2459 9135 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 163 Å2 / Biso mean: 39.5494 Å2 / Biso min: 18.29 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20.67 Å20 Å2
2--1.34 Å20 Å2
3----2.01 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2558 0 44 0 2602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222656
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.9893576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2215317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42723.59117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.9515482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1471517
X-RAY DIFFRACTIONr_chiral_restr0.110.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211967
X-RAY DIFFRACTIONr_mcbond_it2.7581.51590
X-RAY DIFFRACTIONr_mcangle_it4.54622547
X-RAY DIFFRACTIONr_scbond_it2.69731066
X-RAY DIFFRACTIONr_scangle_it4.5394.51029
X-RAY DIFFRACTIONr_rigid_bond_restr2.64632656
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 42 -
Rwork0.276 613 -
all-655 -
obs--98.79 %
Refinement TLS params.Method: refined / Origin x: -40.2677 Å / Origin y: 21.1161 Å / Origin z: 9.8834 Å
111213212223313233
T0.1134 Å2-0.0061 Å2-0.0029 Å2-0.0588 Å2-0.0191 Å2--0.0159 Å2
L0.8218 °20.1619 °2-0.4684 °2-0.2648 °2-0.2655 °2--0.3991 °2
S0.0339 Å °0.036 Å °-0.0147 Å °-0.058 Å °-0.0301 Å °0.0229 Å °0.0241 Å °0.0137 Å °-0.0039 Å °

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