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- PDB-3rny: Crystal structure of human RSK1 C-terminal kinase domain -

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Basic information

Entry
Database: PDB / ID: 3rny
TitleCrystal structure of human RSK1 C-terminal kinase domain
ComponentsRibosomal protein S6 kinase alpha-1
KeywordsTRANSFERASE / protein kinase / autoinhibition
Function / homology
Function and homology information


regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / ribosomal protein S6 kinase activity / CREB phosphorylation / hepatocyte proliferation / positive regulation of hepatic stellate cell activation / Gastrin-CREB signalling pathway via PKC and MAPK / RSK activation / negative regulation of TOR signaling / ERK/MAPK targets ...regulation of translation in response to stress / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / ribosomal protein S6 kinase activity / CREB phosphorylation / hepatocyte proliferation / positive regulation of hepatic stellate cell activation / Gastrin-CREB signalling pathway via PKC and MAPK / RSK activation / negative regulation of TOR signaling / ERK/MAPK targets / Recycling pathway of L1 / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / protein serine/threonine/tyrosine kinase activity / positive regulation of cell differentiation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / chemical synaptic transmission / non-specific serine/threonine protein kinase / intracellular signal transduction / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / synapse / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / magnesium ion binding / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / cytoplasm / cytosol
Similarity search - Function
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 ...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-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLi, D. / Fu, T.-M. / Nan, J. / Su, X.-D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural basis for the autoinhibition of the C-terminal kinase domain of human RSK1.
Authors: Li, D. / Fu, T.M. / Nan, J. / Liu, C. / Li, L.F. / Su, X.D.
History
DepositionApr 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Sep 13, 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_asym_id / _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_asym_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_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: Ribosomal protein S6 kinase alpha-1
B: Ribosomal protein S6 kinase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6914
Polymers77,6452
Non-polymers462
Water77543
1
A: Ribosomal protein S6 kinase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8452
Polymers38,8221
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosomal protein S6 kinase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8452
Polymers38,8221
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-36 kcal/mol
Surface area24470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.860, 143.470, 59.920
Angle α, β, γ (deg.)90.000, 95.770, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribosomal protein S6 kinase alpha-1 / S6K-alpha-1 / 90 kDa ribosomal protein S6 kinase 1 / p90-RSK 1 / p90RSK1 / p90S6K / MAP kinase- ...S6K-alpha-1 / 90 kDa ribosomal protein S6 kinase 1 / p90-RSK 1 / p90RSK1 / p90S6K / MAP kinase-activated protein kinase 1a / MAPK-activated protein kinase 1a / MAPKAP kinase 1a / MAPKAPK-1a / Ribosomal S6 kinase 1 / RSK-1


Mass: 38822.355 Da / Num. of mol.: 2 / Fragment: UNP residues 411-735
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KA1, MAPKAPK1A, RSK1 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: Q15418, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 17.1%(w/v) PEG 3350, 4%(v/v) acetonitrile or 18%(w/v) PEG 3350, 100 mM ammonium formate, 4%(v/v) acetonitrile, vapor diffusion, sitting drop, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.98 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 25637 / Biso Wilson estimate: 52.84 Å2

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QR7

2qr7


Resolution: 2.7→11.98 Å / Cor.coef. Fo:Fc: 0.8912 / Cor.coef. Fo:Fc free: 0.8352 / Occupancy max: 1 / Occupancy min: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 921 5.16 %RANDOM
Rwork0.1882 ---
obs0.1908 17838 --
Displacement parametersBiso max: 146.71 Å2 / Biso mean: 46.3016 Å2 / Biso min: 11.22 Å2
Baniso -1Baniso -2Baniso -3
1--7.0177 Å20 Å2-4.4894 Å2
2---10.634 Å20 Å2
3---17.6517 Å2
Refine analyzeLuzzati coordinate error obs: 0.354 Å
Refinement stepCycle: LAST / Resolution: 2.7→11.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4017 0 2 43 4062
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1391SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes90HARMONIC2
X-RAY DIFFRACTIONt_gen_planes600HARMONIC5
X-RAY DIFFRACTIONt_it4098HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion557SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4530SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4098HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5568HARMONIC21.21
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion20.16
LS refinement shellResolution: 2.7→2.86 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2672 160 5.42 %
Rwork0.2155 2790 -
all0.2182 2950 -
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)
1-0.2556-0.1192.71190.659-1.276610.5826-0.0769-0.0339-0.1028-0.3453-0.3588-0.02260.13820.00110.43570.14510.03450.0441-0.166-0.07070.277310.0678-2.5552-11.0971
20.09080.61430.07934.5784-0.88164.16310.00350.3528-0.0059-0.9202-0.11470.05870.5118-0.32830.1112-0.045-0.0319-0.0091-0.0676-0.07780.23276.396-1.9407-0.7232
31.3170.3049-0.81824.6381.06680.94560.01140.3381-0.3598-0.27690.0006-0.55460.2101-0.1034-0.012-0.3626-0.0018-0.0337-0.3467-0.02880.11076.79180.18749.1904
411.08120.99631.490315.9189-4.04150.188-0.0154-0.23120.0501-0.125-0.1552-0.33520.146-0.01640.1706-0.2584-0.0016-0.0817-0.3728-0.08660.635717.4688-19.195713.3561
53.73250.6240.66870-0.18420.0970.065-0.1528-0.03340.05390.0887-0.3451-0.03440.1946-0.1538-0.2545-0.0257-0.0294-0.1867-0.04840.112219.90659.61118.2407
60.25621.306-1.35715.1348-0.7991.77090.0708-0.6117-0.17450.8592-0.2877-0.38270.35690.12190.2169-0.152-0.0831-0.1746-0.06720.03860.33812.72252.384925.9221
70.16022.49474.84530-5.38429.730.0432-0.199-0.08410.3575-0.20790.1001-0.1364-0.0480.1647-0.2319-0.1567-0.0203-0.04990.01490.33540.13863.421924.8755
80.86671.56130.47940.46181.14413.29540.15970.52470.19160.0513-0.05550.0686-0.22010.2059-0.1042-0.1988-0.0417-0.049-0.12490.0110.239315.201813.004811.832
90.443-6.43322.087.0791.10267.1520.06750.4194-0.10780.0488-0.0445-0.00470.19230.7505-0.0230.00330.1232-0.0312-0.0746-0.0977-0.20976.2867-44.2044-8.9671
100.06161.3417-0.5210-3.50824.28150.03470.0936-0.22860.0036-0.07880.22610.1422-0.07540.04410.36960.0967-0.13610.034-0.03880.1375-5.4424-31.3734-3.1343
111.8672-1.60492.1353.44460.11131.80410.15690.60490.1218-0.6507-0.2552-0.1919-0.31850.44130.0983-0.15050.0315-0.0315-0.0322-0.00610.1057.445-41.13736.1033
12-0.08662.40830.81495.33260.18251.6163-0.09980.23750.5694-0.27380.0360.4428-0.08290.13110.0638-0.21810.0032-0.0766-0.25290.05180.18293.5323-33.70829.6786
130.6161-1.10870.65125.7073-6.68163.82570.0062-0.19620.35510.17580.16990.6752-0.0708-0.2826-0.1761-0.2030.0345-0.071-0.1384-0.01210.3945-1.5439-34.791119.6047
147.5246-1.2191.16990-1.80450.15960.2427-0.5976-0.25710.1891-0.3891-0.2861-0.0774-0.37570.1464-0.1529-0.019-0.0436-0.04770.01580.2494-12.0417-49.264921.8123
155.70422.4769-0.086710.4038-2.09433.50520.2473-0.76530.27580.5448-0.37650.1824-0.1061-0.22610.1292-0.1635-0.00370.0073-0.0583-0.07450.00942.698-41.240729.056
163.20111.07010.47631.7565-0.73391.67750.07080.048-0.11950.1151-0.0890.18150.259-0.3030.0182-0.2070.0075-0.0376-0.1916-0.06570.23220.6771-50.201318.7422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|418 - 459}A418 - 459
2X-RAY DIFFRACTION2{A|460 - 504}A460 - 504
3X-RAY DIFFRACTION3{A|505 - 564}A505 - 564
4X-RAY DIFFRACTION4{A|565 - 592}A565 - 592
5X-RAY DIFFRACTION5{A|593 - 642}A593 - 642
6X-RAY DIFFRACTION6{A|643 - 669}A643 - 669
7X-RAY DIFFRACTION7{A|670 - 680}A670 - 680
8X-RAY DIFFRACTION8{A|681 - 707}A681 - 707
9X-RAY DIFFRACTION9{B|419 - 447}B419 - 447
10X-RAY DIFFRACTION10{B|448 - 461}B448 - 461
11X-RAY DIFFRACTION11{B|462 - 520}B462 - 520
12X-RAY DIFFRACTION12{B|521 - 572}B521 - 572
13X-RAY DIFFRACTION13{B|573 - 609}B573 - 609
14X-RAY DIFFRACTION14{B|610 - 635}B610 - 635
15X-RAY DIFFRACTION15{B|636 - 676}B636 - 676
16X-RAY DIFFRACTION16{B|677 - 708}B677 - 708

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