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- PDB-6g78: RSK4 N-terminal Kinase Domain S232E in complex with AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 6g78
TitleRSK4 N-terminal Kinase Domain S232E in complex with AMP-PNP
ComponentsRibosomal protein S6 kinase alpha-6Ribosome
KeywordsTRANSFERASE / RSK4 / AGC kinase / p90 ribosomal S6 kinases
Function / homology
Function and homology information


negative regulation of embryonic development / negative regulation of mesoderm development / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / ribosomal protein S6 kinase activity / RSK activation / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Recycling pathway of L1 / central nervous system development / negative regulation of ERK1 and ERK2 cascade / fibrillar center ...negative regulation of embryonic development / negative regulation of mesoderm development / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / ribosomal protein S6 kinase activity / RSK activation / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Recycling pathway of L1 / central nervous system development / negative regulation of ERK1 and ERK2 cascade / fibrillar center / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / nucleolus / magnesium ion binding / signal transduction / mitochondrion / nucleoplasm / ATP binding / cytosol / cytoplasm
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. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase 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. / 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
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Ribosomal protein S6 kinase alpha-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPrischi, F. / Ali, M.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC33269/A11161 United Kingdom
CitationJournal: Sci Transl Med / Year: 2021
Title: Repurposed floxacins targeting RSK4 prevent chemoresistance and metastasis in lung and bladder cancer.
Authors: Chrysostomou, S. / Roy, R. / Prischi, F. / Thamlikitkul, L. / Chapman, K.L. / Mufti, U. / Peach, R. / Ding, L. / Hancock, D. / Moore, C. / Molina-Arcas, M. / Mauri, F. / Pinato, D.J. / ...Authors: Chrysostomou, S. / Roy, R. / Prischi, F. / Thamlikitkul, L. / Chapman, K.L. / Mufti, U. / Peach, R. / Ding, L. / Hancock, D. / Moore, C. / Molina-Arcas, M. / Mauri, F. / Pinato, D.J. / Abrahams, J.M. / Ottaviani, S. / Castellano, L. / Giamas, G. / Pascoe, J. / Moonamale, D. / Pirrie, S. / Gaunt, C. / Billingham, L. / Steven, N.M. / Cullen, M. / Hrouda, D. / Winkler, M. / Post, J. / Cohen, P. / Salpeter, S.J. / Bar, V. / Zundelevich, A. / Golan, S. / Leibovici, D. / Lara, R. / Klug, D.R. / Yaliraki, S.N. / Barahona, M. / Wang, Y. / Downward, J. / Skehel, J.M. / Ali, M.M.U. / Seckl, M.J. / Pardo, O.E.
History
DepositionApr 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_validate_symm_contact ...diffrn_source / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Aug 11, 2021Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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-6
B: Ribosomal protein S6 kinase alpha-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5584
Polymers70,5462
Non-polymers1,0122
Water1,53185
1
A: Ribosomal protein S6 kinase alpha-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7792
Polymers35,2731
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosomal protein S6 kinase alpha-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7792
Polymers35,2731
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.015, 110.614, 66.559
Angle α, β, γ (deg.)90.000, 90.220, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribosomal protein S6 kinase alpha-6 / Ribosome / S6K-alpha-6 / 90 kDa ribosomal protein S6 kinase 6 / p90RSK6 / Ribosomal S6 kinase 4 / RSK-4 / pp90RSK4


Mass: 35272.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KA6, RSK4 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UK32, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.95 Å3/Da / Density % sol: 58.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20 % PEG 6000, 0.1 M TRIS pH8, 2 mM Zinc chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97948 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.28
ReflectionResolution: 2.5→28.52 Å / Num. obs: 26061 / % possible obs: 99.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.025 / Net I/σ(I): 2.36
Reflection shellResolution: 2.5→2.589 Å / Num. unique obs: 857 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G77

6g77


Resolution: 2.5→28.515 Å / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 29.84 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2396 1263 4.85 %
Rwork0.2259 24772 -
obs0.2265 26055 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.71 Å2 / Biso mean: 37.2913 Å2 / Biso min: 18.3 Å2
Refinement stepCycle: final / Resolution: 2.5→28.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4505 0 62 85 4652
Biso mean--47.5 34.86 -
Num. residues----564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064671
X-RAY DIFFRACTIONf_angle_d0.9686313
X-RAY DIFFRACTIONf_chiral_restr0.046700
X-RAY DIFFRACTIONf_plane_restr0.004788
X-RAY DIFFRACTIONf_dihedral_angle_d16.1431731
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5006-2.60070.31041200.31572766288696
2.6007-2.7190.33491450.30942746289195
2.719-2.86220.34661300.27832727285795
2.8622-3.04130.31191460.25212758290495
3.0413-3.27590.26161590.25522714287394
3.2759-3.60490.23411280.22662749287795
3.6049-4.12520.22211500.20082753290395
4.1252-5.19220.19471430.17632767291095
5.1922-28.51690.18631380.21532792293095

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