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- PDB-4l3j: Crystal structures of human p70S6K1 kinase domain -

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Basic information

Entry
Database: PDB / ID: 4l3j
TitleCrystal structures of human p70S6K1 kinase domain
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 / protein phosphatase 2A binding / positive regulation of translation / 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: 2.1 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 6, 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
Revision 1.3Nov 8, 2023Group: 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 / 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)34,7933
Polymers34,3371
Non-polymers4562
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.511, 70.511, 150.484
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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: 34337.094 Da / Num. of mol.: 1
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

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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: 2.82 Å3/Da / Density % sol: 56.34 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: CCD ADSC unsupported-q315 / Detector: CCD / Date: Jun 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 22617

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A62

3a62


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.57 / SU B: 14.348 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2546 1118 5 %RANDOM
Rwork0.2103 ---
obs0.2125 22302 97.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 129.48 Å2 / Biso mean: 47.2591 Å2 / Biso min: 18.06 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å20 Å20 Å2
2--1.57 Å20 Å2
3----3.15 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 29 121 2455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222388
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.9883221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3545290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48523.5100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.57215434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5891514
X-RAY DIFFRACTIONr_chiral_restr0.1260.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211771
X-RAY DIFFRACTIONr_mcbond_it2.3531.51443
X-RAY DIFFRACTIONr_mcangle_it4.17722313
X-RAY DIFFRACTIONr_scbond_it4.6713945
X-RAY DIFFRACTIONr_scangle_it7.0934.5908
X-RAY DIFFRACTIONr_rigid_bond_restr3.4932388
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 87 -
Rwork0.236 1558 -
all-1645 -
obs--98.74 %
Refinement TLS params.Method: refined / Origin x: 23.2796 Å / Origin y: -13.423 Å / Origin z: 6.0683 Å
111213212223313233
T0.1506 Å20.0012 Å2-0.0083 Å2-0.1347 Å20.0084 Å2--0.0371 Å2
L0.0176 °20.0492 °20.061 °2-0.1999 °2-0.1538 °2--0.2534 °2
S0.0083 Å °0.0297 Å °0.019 Å °-0.0091 Å °-0.0264 Å °-0.0582 Å °0.055 Å °0.0212 Å °0.0182 Å °

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