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- PDB-2qr7: 2.0A X-ray structure of C-terminal kinase domain of p90 ribosomal... -

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Basic information

Entry
Database: PDB / ID: 2qr7
Title2.0A X-ray structure of C-terminal kinase domain of p90 ribosomal S6 kinase 2: Se-Met derivative
ComponentsRibosomal protein S6 kinase alpha-3
KeywordsTRANSFERASE / kinase domain / RSK2 / autoinhibitory / ATP-binding / Nucleotide-binding / Phosphorylation / Serine/threonine-protein kinase
Function / homology
Function and homology information


RSK activation / CREB phosphorylation / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / Gastrin-CREB signalling pathway via PKC and MAPK / Senescence-Associated Secretory Phenotype (SASP) / ribosomal protein S6 kinase activity / ERK/MAPK targets / toll-like receptor signaling pathway / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to lipopolysaccharide ...RSK activation / CREB phosphorylation / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / Gastrin-CREB signalling pathway via PKC and MAPK / Senescence-Associated Secretory Phenotype (SASP) / ribosomal protein S6 kinase activity / ERK/MAPK targets / toll-like receptor signaling pathway / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to lipopolysaccharide / non-specific serine/threonine protein kinase / intracellular signal transduction / cell cycle / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / protein kinase binding / magnesium ion binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein S6 kinase alpha-3, C-terminal catalytic domain / Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / 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 ...Ribosomal protein S6 kinase alpha-3, C-terminal catalytic domain / Ribosomal S6 kinase, N-terminal catalytic domain / Ribosomal protein S6 kinase II / 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
Ribosomal protein S6 kinase alpha-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMalakhova, M. / Tereshko, V. / Dong, Z.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural basis for activation of the autoinhibitory C-terminal kinase domain of p90 RSK2.
Authors: Malakhova, M. / Tereshko, V. / Lee, S.Y. / Yao, K. / Cho, Y.-Y. / Bode, A. / Dong, Z.
History
DepositionJul 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / 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_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.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

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Assembly

Deposited unit
A: Ribosomal protein S6 kinase alpha-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8302
Polymers38,8071
Non-polymers231
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.585, 46.585, 293.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Ribosomal protein S6 kinase alpha-3 / S6K-alpha 3 / 90 kDa ribosomal protein S6 kinase 3 / p90-RSK 3 / Ribosomal S6 kinase 2 / RSK-2 / ...S6K-alpha 3 / 90 kDa ribosomal protein S6 kinase 3 / p90-RSK 3 / Ribosomal S6 kinase 2 / RSK-2 / pp90RSK2 / MAP kinase-activated protein kinase 1b / MAPKAPK1B


Mass: 38807.191 Da / Num. of mol.: 1 / Mutation: K591E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rps6ka3, Rps6ka-rs1, Rsk2 / Plasmid: pET-46 EK/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codon Plus (DE3)-RILP
References: UniProt: P18654, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.06 Å3/Da / Density % sol: 40.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 7.5%-10% PEG3350, 50mM Ammonium sulfate, 0.1M Hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97936 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 1, 2006 / Details: ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 23160 / Num. obs: 23160 / % possible obs: 99.9 % / Observed criterion σ(F): 23160 / Observed criterion σ(I): 23160 / Redundancy: 7.7 % / Biso Wilson estimate: 45.9 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 36.84
Reflection shellResolution: 2→2.06 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.744 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): -3 / ESU R: 0.186 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23776 1187 5.1 %RANDOM
Rwork0.20276 ---
all0.2045 23160 --
obs0.2045 23160 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.84 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å20 Å2
2--1.27 Å20 Å2
3----2.54 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2365 0 1 91 2457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192427
X-RAY DIFFRACTIONr_bond_other_d0.0010.021638
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.8873293
X-RAY DIFFRACTIONr_angle_other_deg0.8342.1623998
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5935297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72124.159113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.64415417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0331514
X-RAY DIFFRACTIONr_chiral_restr0.0750.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022690
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02488
X-RAY DIFFRACTIONr_nbd_refined0.2320.2494
X-RAY DIFFRACTIONr_nbd_other0.2050.21636
X-RAY DIFFRACTIONr_nbtor_refined0.1940.21199
X-RAY DIFFRACTIONr_nbtor_other0.090.21088
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.278
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0710.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1260.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2750.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8991.51484
X-RAY DIFFRACTIONr_mcbond_other0.241.5602
X-RAY DIFFRACTIONr_mcangle_it1.64622401
X-RAY DIFFRACTIONr_scbond_it2.7753975
X-RAY DIFFRACTIONr_scangle_it3.9484.5892
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 90 -
Rwork0.208 1549 -
obs--99.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.19251.055-0.10192.55520.12572.34140.0691-0.23980.18780.1919-0.1326-0.1317-0.5885-0.03390.0634-0.02380.0942-0.05770.0112-0.061-0.148534.481537.2358132.6625
21.3162-0.34850.4411.38-0.19151.4455-0.1139-0.2277-0.01460.11170.17570.09170.0021-0.2029-0.0618-0.14210.04240.03390.04330.044-0.030316.185721.7478123.7432
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA417 - 49519 - 97
2X-RAY DIFFRACTION1AB - C1000 - 10121 - 12
3X-RAY DIFFRACTION2AA496 - 71498 - 316
4X-RAY DIFFRACTION2AC1013 - 109113 - 91

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