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- PDB-7up8: Crystal structure of C-terminal Domain of MSK1 in complex with co... -

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Basic information

Entry
Database: PDB / ID: 7up8
TitleCrystal structure of C-terminal Domain of MSK1 in complex with covalently bound pyrrolopyrimidine compound 27 (co-crystal)
ComponentsRibosomal protein S6 kinase alpha-5
KeywordsTRANSFERASE / Msk1 / C-terminal domain / PROTEIN KINASE / PHOSPHORYLATION
Function / homology
Function and homology information


histone H3S28 kinase activity / histone H2AS1 kinase activity / positive regulation of CREB transcription factor activity / CREB phosphorylation / histone H3S10 kinase activity / interleukin-1-mediated signaling pathway / negative regulation of cytokine production / regulation of postsynapse organization / ERK/MAPK targets / Recycling pathway of L1 ...histone H3S28 kinase activity / histone H2AS1 kinase activity / positive regulation of CREB transcription factor activity / CREB phosphorylation / histone H3S10 kinase activity / interleukin-1-mediated signaling pathway / negative regulation of cytokine production / regulation of postsynapse organization / ERK/MAPK targets / Recycling pathway of L1 / post-translational protein modification / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / axon guidance / positive regulation of NF-kappaB transcription factor activity / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / intracellular signal transduction / inflammatory response / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
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 ...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
Chem-O10 / Ribosomal protein S6 kinase alpha-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsYano, J.K. / Abendroth, J. / Hall, A.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Acs Med.Chem.Lett. / Year: 2022
Title: Discovery and Characterization of a Novel Series of Chloropyrimidines as Covalent Inhibitors of the Kinase MSK1.
Authors: Hall, A. / Abendroth, J. / Bolejack, M.J. / Ceska, T. / Dell'Aiera, S. / Ellis, V. / Fox 3rd, D. / Francois, C. / Muruthi, M.M. / Prevel, C. / Poullennec, K. / Romanov, S. / Valade, A. / ...Authors: Hall, A. / Abendroth, J. / Bolejack, M.J. / Ceska, T. / Dell'Aiera, S. / Ellis, V. / Fox 3rd, D. / Francois, C. / Muruthi, M.M. / Prevel, C. / Poullennec, K. / Romanov, S. / Valade, A. / Vanbellinghen, A. / Yano, J. / Geraerts, M.
History
DepositionApr 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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-5
B: Ribosomal protein S6 kinase alpha-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9594
Polymers69,3382
Non-polymers6212
Water543
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A: Ribosomal protein S6 kinase alpha-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9792
Polymers34,6691
Non-polymers3111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosomal protein S6 kinase alpha-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9792
Polymers34,6691
Non-polymers3111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.520, 90.910, 136.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 415 through 514 or (resid 515...
d_2ens_1(chain "B" and (resid 415 through 525 or resid 527...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LYSMETA1 - 111
d_12ens_1LYSLEUA113 - 231
d_13ens_1TYRASNA233 - 273
d_14ens_1266266B
d_21ens_1LYSMETC1 - 111
d_22ens_1LYSASPC113 - 140
d_23ens_1LEUGLNC142 - 181
d_24ens_1CYSLEUC184 - 234
d_25ens_1TYRASNC236 - 276
d_26ens_1266266D

NCS oper: (Code: givenMatrix: (0.999883185308, -0.0131042016636, -0.00786737797896), (-0.0149982587484, -0.940347292583, -0.339885306488), (-0.00294414198354, 0.339963599861, -0.940433986411)Vector: - ...NCS oper: (Code: given
Matrix: (0.999883185308, -0.0131042016636, -0.00786737797896), (-0.0149982587484, -0.940347292583, -0.339885306488), (-0.00294414198354, 0.339963599861, -0.940433986411)
Vector: -14.6720724185, 122.324092223, 109.905787867)

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Components

#1: Protein Ribosomal protein S6 kinase alpha-5 / S6K-alpha-5 / 90 kDa ribosomal protein S6 kinase 5 / Nuclear mitogen- and stress-activated protein ...S6K-alpha-5 / 90 kDa ribosomal protein S6 kinase 5 / Nuclear mitogen- and stress-activated protein kinase 1 / RSK-like protein kinase / RSKL


Mass: 34668.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KA5, MSK1 / Production host: Escherichia coli (E. coli)
References: UniProt: O75582, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-O10 / (5M)-5-(5-bromo-2-chloropyrimidin-4-yl)-5H-pyrrolo[3,2-d]pyrimidine


Mass: 310.537 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H5BrClN5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Plate 320267f8, puck cnl-6-9.Screen:Morpheus_D8_F8_G8_Index_E7. To prepare the ligand complex, PID7059-1 was exchanged to 25 mM HEPES pH 7.5, 150 mM NaCl, 5% glycerol, 1 mM BME (dillution ...Details: Plate 320267f8, puck cnl-6-9.Screen:Morpheus_D8_F8_G8_Index_E7. To prepare the ligand complex, PID7059-1 was exchanged to 25 mM HEPES pH 7.5, 150 mM NaCl, 5% glycerol, 1 mM BME (dillution buffer) using a GE (GE28-9180-04) spin column. The protein was diluted to 1 mg/ml in dilution bufffer and 150 ?M UCB1710266 in 100% DMSO_D6 was added. The complex was incubated at 4 C for an hour, then excess ligand was removed by dialysis using a D-tube dialyzer in 250 ml dilution buffer, overnight at 4 ?C. The following day the protein was concentrated to 10.1 mg/ml and setup 200:100 ul protein:well solution. Crystals were flash frozen in 100% well solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 8, 2021
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 14778 / % possible obs: 99.6 % / Redundancy: 4.002 % / Biso Wilson estimate: 50.492 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.119 / Χ2: 0.921 / Net I/σ(I): 10.99
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.9-2.984.1030.5592.710710.8240.643100
2.98-3.064.1180.5412.7410480.8280.62399.6
3.06-3.154.0880.4083.6510010.8810.469100
3.15-3.244.1130.3124.5410140.9290.35899.8
3.24-3.354.0780.2395.869490.9520.275100
3.35-3.474.0810.197.099430.9750.21999.9
3.47-3.64.0730.1578.168870.9830.18199.8
3.6-3.743.9910.12410.358750.9850.14399.8
3.74-3.914.0180.10112.118360.9910.11799.9
3.91-4.14.0180.08414.027870.9910.09799.7
4.1-4.323.9960.06916.247790.9950.0899.9
4.32-4.593.9690.06117.817150.9960.07199.7
4.59-4.93.9540.06217.496770.9950.07299.9
4.9-5.293.9690.06317.486530.9960.07299.7
5.29-5.83.9430.07115.835950.9950.08299.7
5.8-6.483.8920.06716.715450.9940.07899.8
6.48-7.493.8390.05718.594830.9970.06699.4
7.49-9.173.7270.04323.424030.9960.0598.8
9.17-12.973.6230.03825.923340.9950.04598.5
12.97-503.1420.03124.291830.9980.03791.5

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Processing

Software
NameVersionClassification
PHENIXphenix 1.21refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house model

Resolution: 2.9→48.2 Å / SU ML: 0.388 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3196
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2625 1544 10.45 %0
Rwork0.1863 13228 --
obs0.1942 14772 99.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.99 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4398 0 32 3 4433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00544538
X-RAY DIFFRACTIONf_angle_d0.786094
X-RAY DIFFRACTIONf_chiral_restr0.0464668
X-RAY DIFFRACTIONf_plane_restr0.0057767
X-RAY DIFFRACTIONf_dihedral_angle_d13.96181698
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.897134924144 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.990.2811370.22881187X-RAY DIFFRACTION99.7
2.99-3.10.35481320.26151168X-RAY DIFFRACTION99.85
3.1-3.220.33071440.26321196X-RAY DIFFRACTION99.85
3.22-3.370.31091500.20911162X-RAY DIFFRACTION100
3.37-3.550.29841360.20721168X-RAY DIFFRACTION99.85
3.55-3.770.30471350.20361202X-RAY DIFFRACTION99.78
3.77-4.060.24961430.17951201X-RAY DIFFRACTION99.78
4.06-4.470.22791270.14971203X-RAY DIFFRACTION99.77
4.47-5.120.22611450.14091233X-RAY DIFFRACTION99.86
5.12-6.440.24971400.18191237X-RAY DIFFRACTION99.71
6.45-48.20.22841550.17911271X-RAY DIFFRACTION97.94
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)
16.61090520189-1.69327749765-4.704810777753.811641571271.44232116127.61260084125-0.0420928991099-0.3145966437710.1249708184770.03015135421390.128275753074-0.5777088837650.1455940446880.3871431556660.0007552010233450.3117435226350.026213153612-0.1081367231270.378772318935-0.09666294929290.40864381062634.982810666560.652049090349.5956930974
28.85206530256-3.27188917782-1.284279885614.987524085392.637240026861.96002516739-0.5623482997180.4304563925110.2539660556130.389733539506-0.0260113777840.894149680339-0.414527847575-1.015283524410.6867938238840.6136459099970.0931978767675-0.01903754024860.684770977652-0.09975814145161.0140289810519.039975866173.026214670252.9149217411
34.65534055758-0.491899405280.01136517359264.825811723251.943661709242.702331826260.1309428545760.04590642349780.54812717659-0.406531497237-0.1166324097370.95882367865-0.821338272588-0.3232242344990.07137340488210.4634689917330.0976809957997-0.05749129066860.6318152102890.06245420184250.39016848794410.425005708143.000749220785.5523248749
48.675443760651.4205629466-1.897160149711.62436055749-0.9794437126864.28513330615-0.05004298195440.006143388571490.0260809461363-0.007233961207680.05002227023640.0584418866330.0435551948543-0.312310223702-0.000986452990560.3728467360150.025762578783-0.01149323728530.341274687042-0.03709199713460.24418102373220.422267352636.63990661688.7504365838
57.214988022542.17474747613-4.199617957741.0879456347-1.135324117423.692041565190.08008785860420.1611535943910.187653072345-0.1205555319920.001254837145240.0228772024623-0.1479933326580.00614838813718-0.09907196672730.3759670944020.0240724904431-0.01922287708250.228109698762-0.03432623470020.31755557855636.42458050741.110342479881.2981848488
66.261492281750.482422849958-3.697001458571.91524686720.0383579432836.62605961393-0.413957731844-0.173232491522-0.134015097795-0.08381804293410.2915390128290.2116503716341.51690734459-0.1278763798510.1478047126120.4783833116110.0405121993308-0.00733248899290.287604286735-0.01114877156180.36355886759238.634768313129.841867162280.9550259973
76.388657525041.959709083433.118981573072.162993336192.188288747413.29556684715-0.607110364620.88735694217-0.60828766822-1.005727166020.17391892042-0.2633198765780.873436025790.5425163159450.4373371736630.9906406291580.09024935868540.1657010238740.6091541167140.02668436773970.49756968654845.644887291228.486986974264.6844703698
88.3195564378-0.4599790734813.251892788067.32291984458-0.4488888885276.86158527740.54861027537-0.0566104524602-0.647053779681-0.0857485940117-0.253901285471-0.212324631480.6436040493190.152999177173-0.1942606263320.4383826136410.143953830257-0.02203609563550.4430669494920.04904362909360.42603904272952.15637306628.588469658279.6064116273
99.04390210682-1.530464599887.20479982865.82686493765-3.014369833048.3436235774-0.9153924322880.7703238673790.9512729082760.10866538522-0.189470152457-0.691199153157-0.9513877808271.101499852590.9430173516050.401514339972-0.0132740608440.03357196381760.5206245250870.02272270993690.38705165506950.187660282644.076564787172.7342442311
106.190192501370.6272624556941.803440688830.128119883039-0.1317032329632.02093949889-0.3951993239890.5831388769710.3273895006080.556311922679-0.3115815340670.3058767590120.692714872204-1.714800626350.599424592430.8857703527650.04450309132030.1149574137091.10129040151-0.301337262881.074275910833.853992728429.822844117968.6682587981
114.00424903030.416000514185-2.640304219636.387365099741.167385762812.06841114371-0.01293050629480.0672118718416-0.435630455730.0769995526519-0.2309067014250.289083156180.647993471821-0.1393344639540.2360449994110.3487772173990.07326566798660.07003737730180.517674642603-0.05265300055740.498848242742-5.5159597872952.117999472643.8375482407
126.335145269150.7251637987350.239864312952.013667010051.243417492757.80306873884-0.182783056662-0.565307549376-0.1318783149010.625863374538-0.1278290712220.196575798260.2036610173670.3864735784510.307042796460.329872539747-0.003901407259810.02516199996810.54270330516-0.006550884023260.37805028920.1219668955453.261069354845.068389065
135.310969307490.1769882056542.343759307350.4064937513230.8063348004233.577278840080.000296688767872-0.0189282975090.05759504088020.0138617028272-0.09962107008080.0411745478730.211196702748-0.1164301811860.1203169250230.3760996545310.031844298510.04204500413250.268851490776-0.03357242148020.3242930249589.6072631522356.873060986642.2206388695
146.749268809291.600704104882.690661525672.550801276110.5560761079854.81597467814-0.0472249445942-0.2799021255610.04344446757130.303049886472-0.0403003005457-0.04596186776320.243707366674-0.0895505142620.09730952943790.3564662190880.11337057177-0.009629868095290.395151045783-0.03720097612260.31329867084622.980292090156.847314851544.8090632288
156.033702596150.1182288419742.487925911174.504556376330.499127087013.64156268994-0.385744788575-0.04381093503950.777752177622-0.35003238917-0.0287271084016-0.0973563704793-0.443616120188-0.4817392612670.4425291519250.3568520760020.05113281709450.006563722923690.338288534829-0.03222022304430.38296960685622.828517673966.34860518143.9037688246
163.29420397566-2.066987081360.6431573137019.019097109760.4897041915070.2700779414550.0327793612668-0.7019873795990.1714038455551.202323826440.01575171367890.724570343812-1.110238502120.0968603693556-0.06523291094750.6642289819150.1999345699760.07300147291230.557928030835-0.06475876443450.64274702027925.679693052477.373656541357.5699786564
176.4430465097-3.2792155385-1.348154634478.72765632032-0.9389130335336.30176351174-0.54242315887-0.7368717702850.3170607674811.021607436870.247814276839-0.286487106969-0.178630290540.5007331059540.3935604691390.4518398625490.0246719602228-0.07678737990940.438908073788-0.1052537516250.48238693796337.084800412966.503025574656.3217043691
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 668 through 706 )BC668 - 706222 - 260
22chain 'B' and (resid 707 through 726 )BC707 - 726261 - 280
33chain 'A' and (resid 415 through 432 )AA415 - 4321 - 18
44chain 'A' and (resid 433 through 492 )AA433 - 49219 - 78
55chain 'A' and (resid 493 through 563 )AA493 - 56379 - 145
66chain 'A' and (resid 564 through 616 )AA564 - 616146 - 174
77chain 'A' and (resid 617 through 656 )AA617 - 656175 - 207
88chain 'A' and (resid 657 through 682 )AA657 - 682208 - 233
99chain 'A' and (resid 683 through 706 )AA683 - 706234 - 257
1010chain 'A' and (resid 707 through 722 )AA707 - 722258 - 273
1111chain 'B' and (resid 415 through 432 )BC415 - 4321 - 18
1212chain 'B' and (resid 433 through 450 )BC433 - 45019 - 36
1313chain 'B' and (resid 451 through 517 )BC451 - 51737 - 103
1414chain 'B' and (resid 518 through 563 )BC518 - 563104 - 146
1515chain 'B' and (resid 564 through 616 )BC564 - 616147 - 175
1616chain 'B' and (resid 617 through 642 )BC617 - 642176 - 196
1717chain 'B' and (resid 643 through 667 )BC643 - 667197 - 221

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