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- PDB-3a61: Crystal structure of unphosphorylated p70S6K1 (Form II) -

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Basic information

Entry
Database: PDB / ID: 3a61
TitleCrystal structure of unphosphorylated p70S6K1 (Form II)
ComponentsRibosomal protein S6 kinase beta-1
KeywordsTRANSFERASE / Kinase / Kinase domain / Inactive / Active / Ribosomal S6 kinase / Activation / Alternative initiation / ATP-binding / Cell junction / Cytoplasm / Nucleotide-binding / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase / Synapse / Synaptosome
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 D-glucose import / ribosomal protein S6 kinase activity / response to L-leucine / cellular response to nutrient / response to glucagon / positive regulation of smooth muscle cell migration ...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 D-glucose import / ribosomal protein S6 kinase activity / response to L-leucine / cellular response to nutrient / response to glucagon / positive regulation of smooth muscle cell migration / response to testosterone / phosphatidylinositol-mediated signaling / mTORC1-mediated signalling / germ cell development / skeletal muscle contraction / TOR signaling / behavioral fear response / response to tumor necrosis factor / positive regulation of translational initiation / response to glucose / long-term memory / response to mechanical stimulus / negative regulation of insulin receptor signaling pathway / protein serine/threonine/tyrosine kinase activity / positive regulation of TORC1 signaling / positive regulation of mitotic cell cycle / cellular response to dexamethasone stimulus / response to nutrient levels / protein phosphatase 2A binding / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of translation / PDZ domain binding / positive regulation of smooth muscle cell proliferation / peptide binding / modulation of chemical synaptic transmission / cellular response to growth factor stimulus / cellular response to type II interferon / response to toxic substance / cellular response to insulin stimulus / G1/S transition of mitotic cell cycle / cell migration / peptidyl-serine phosphorylation / response to ethanol / mitochondrial outer membrane / postsynapse / response to lipopolysaccharide / non-specific serine/threonine protein kinase / protein kinase activity / neuron projection / response to xenobiotic stimulus / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / negative regulation of apoptotic process / 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
STAUROSPORINE / Ribosomal protein S6 kinase beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.43 Å
AuthorsSunami, T. / Byrne, N. / Diehl, R.E. / Funabashi, K. / Hall, D.L. / Ikuta, M. / Patel, S.B. / Shipman, J.M. / Smith, R.F. / Takahashi, I. ...Sunami, T. / Byrne, N. / Diehl, R.E. / Funabashi, K. / Hall, D.L. / Ikuta, M. / Patel, S.B. / Shipman, J.M. / Smith, R.F. / Takahashi, I. / Zugay-Murphy, J. / Iwasawa, Y. / Lumb, K.J. / Munshi, S.K. / Sharma, S.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural basis of human p70 ribosomal S6 kinase-1 regulation by activation loop phosphorylation.
Authors: Sunami, T. / Byrne, N. / Diehl, R.E. / Funabashi, K. / Hall, D.L. / Ikuta, M. / Patel, S.B. / Shipman, J.M. / Smith, R.F. / Takahashi, I. / Zugay-Murphy, J. / Iwasawa, Y. / Lumb, K.J. / Munshi, S.K. / Sharma, S.
History
DepositionAug 18, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / 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: Ribosomal protein S6 kinase beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4032
Polymers36,9371
Non-polymers4671
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.636, 63.014, 98.349
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribosomal protein S6 kinase beta-1 / Ribosomal protein S6 kinase I / S6K1 / S6K / 70 kDa ribosomal protein S6 kinase 1 / p70 S6 kinase ...Ribosomal protein S6 kinase I / S6K1 / S6K / 70 kDa ribosomal protein S6 kinase 1 / p70 S6 kinase alpha / p70(S6K)-alpha / p70-S6K / P70S6K / p70-alpha


Mass: 36936.641 Da / Num. of mol.: 1 / Fragment: UNP residues 75-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVL1392 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P23443, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-STU / STAUROSPORINE


Mass: 466.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM

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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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis-Tris, pH 5.5, 0.2M lithium sulfate, 30% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→30.01 Å / Num. obs: 5002 / % possible obs: 99.8 % / Redundancy: 6.8 % / Rsym value: 0.094 / Net I/σ(I): 10.5
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 7 % / Mean I/σ(I) obs: 7.19 / Rsym value: 0.324 / % possible all: 99.8

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Processing

Software
NameClassification
CrystalCleardata collection
AMoREphasing
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: p70S6K1 homology model based on the published RSK1 structure; PDB ENTRY 2Z7R

2z7r


Resolution: 3.43→30.01 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 788602.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.349 478 10.6 %RANDOM
Rwork0.265 ---
obs0.274 4520 89.8 %-
all-4965 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.2132 Å2 / ksol: 0.38355 e/Å3
Displacement parametersBiso mean: 24.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å20 Å20 Å2
2---11.32 Å20 Å2
3---9.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 3.43→30.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 35 0 2066
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.571.5
X-RAY DIFFRACTIONc_mcangle_it2.772
X-RAY DIFFRACTIONc_scbond_it1.622
X-RAY DIFFRACTIONc_scangle_it2.742.5
LS refinement shellResolution: 3.4→3.61 Å / Rfactor Rfree error: 0.056 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.404 52 10.2 %
Rwork0.321 458 -
obs--61.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2stu.paramstu.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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