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- PDB-1nxk: Crystal structure of staurosporine bound to MAP KAP kinase 2 -

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Basic information

Entry
Database: PDB / ID: 1nxk
TitleCrystal structure of staurosporine bound to MAP KAP kinase 2
ComponentsMAP kinase-activated protein kinase 2
KeywordsTRANSFERASE / protein kinase / mk2 / phosphorylation / staurosporine
Function / homology
Function and homology information


macropinocytosis / calcium-dependent protein serine/threonine kinase activity / CREB phosphorylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / leukotriene metabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / calcium/calmodulin-dependent protein kinase activity ...macropinocytosis / calcium-dependent protein serine/threonine kinase activity / CREB phosphorylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / leukotriene metabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / calcium/calmodulin-dependent protein kinase activity / regulation of interleukin-6 production / mitogen-activated protein kinase binding / positive regulation of macrophage cytokine production / 3'-UTR-mediated mRNA stabilization / toll-like receptor signaling pathway / p38MAPK cascade / inner ear development / cellular response to vascular endothelial growth factor stimulus / Regulation of HSF1-mediated heat shock response / vascular endothelial growth factor receptor signaling pathway / regulation of cellular response to heat / p38MAPK events / regulation of mRNA stability / response to cytokine / activated TAK1 mediates p38 MAPK activation / Regulation of TNFR1 signaling / VEGFA-VEGFR2 Pathway / positive regulation of tumor necrosis factor production / MAPK cascade / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / response to lipopolysaccharide / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / calmodulin binding / protein kinase activity / intracellular signal transduction / protein phosphorylation / inflammatory response / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / DNA damage response / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
MAP kinase activated protein kinase, C-terminal / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...MAP kinase activated protein kinase, C-terminal / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / MAP kinase-activated protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsUnderwood, K.W. / Parris, K.D. / Federico, E. / Mosyak, L. / Czerwinski, R.M. / Shane, T. / Taylor, M. / Svenson, K. / Liu, Y. / Hsiao, C.L. ...Underwood, K.W. / Parris, K.D. / Federico, E. / Mosyak, L. / Czerwinski, R.M. / Shane, T. / Taylor, M. / Svenson, K. / Liu, Y. / Hsiao, C.L. / Wolfrom, S. / Malakian, K. / Telliez, J.B. / Lin, L.L. / Kriz, R.W. / Seehra, J. / Somers, W.S. / Stahl, M.L.
CitationJournal: Structure / Year: 2003
Title: Catalytically active MAP KAP kinase 2 structures in complex with staurosporine and ADP reveal differences with the autoinhibited enzyme
Authors: Underwood, K.W. / Parris, K.D. / Federico, E. / Mosyak, L. / Czerwinski, R.M. / Shane, T. / Taylor, M. / Svenson, K. / Liu, Y. / Hsiao, C.L. / Wolfrom, S. / Maguire, M. / Malakian, K. / ...Authors: Underwood, K.W. / Parris, K.D. / Federico, E. / Mosyak, L. / Czerwinski, R.M. / Shane, T. / Taylor, M. / Svenson, K. / Liu, Y. / Hsiao, C.L. / Wolfrom, S. / Maguire, M. / Malakian, K. / Telliez, J.B. / Lin, L.L. / Kriz, R.W. / Seehra, J. / Somers, W.S. / Stahl, M.L.
History
DepositionFeb 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: MAP kinase-activated protein kinase 2
B: MAP kinase-activated protein kinase 2
C: MAP kinase-activated protein kinase 2
D: MAP kinase-activated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,82810
Polymers184,7704
Non-polymers2,0586
Water75742
1
A: MAP kinase-activated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6592
Polymers46,1921
Non-polymers4671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MAP kinase-activated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8514
Polymers46,1921
Non-polymers6593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MAP kinase-activated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6592
Polymers46,1921
Non-polymers4671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: MAP kinase-activated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6592
Polymers46,1921
Non-polymers4671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: MAP kinase-activated protein kinase 2
B: MAP kinase-activated protein kinase 2
C: MAP kinase-activated protein kinase 2
D: MAP kinase-activated protein kinase 2
hetero molecules

A: MAP kinase-activated protein kinase 2
B: MAP kinase-activated protein kinase 2
C: MAP kinase-activated protein kinase 2
D: MAP kinase-activated protein kinase 2
hetero molecules

A: MAP kinase-activated protein kinase 2
B: MAP kinase-activated protein kinase 2
C: MAP kinase-activated protein kinase 2
D: MAP kinase-activated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)560,48430
Polymers554,31012
Non-polymers6,17518
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area57660 Å2
ΔGint-379 kcal/mol
Surface area137420 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)160.202, 160.202, 133.481
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
MAP kinase-activated protein kinase 2 / MAPK-activated protein kinase 2 / MAPKAP kinase 2 / MAPKAPK-2


Mass: 46192.473 Da / Num. of mol.: 4 / Fragment: MK2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAPK2 / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P49137, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical
ChemComp-STU / STAUROSPORINE


Mass: 466.531 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2M ammonium sulfate, 100 mM HEPES pH 7.5, 2% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
220 mMHEPES1reservoirpH7.5
3200 mM1reservoirNaCl
410 mMdithiothreitol1reservoir
55 mM1reservoirMgCl2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.211.1
SYNCHROTRONALS 5.0.220.95666, 0.97926, 0.97955
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2002 / Details: Double crystal Si(111)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2Double crystal Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.956661
30.979261
40.979551
ReflectionResolution: 2.7→50 Å / Num. all: 53383 / Num. obs: 52352 / % possible obs: 98.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 20.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.01 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 1.6 / Num. unique all: 4467 / % possible all: 84.1
Reflection
*PLUS
% possible obs: 100 % / Num. measured all: 215726
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.889 / SU B: 12.576 / SU ML: 0.249 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.589 / ESU R Free: 0.331
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.27442 2634 5 %RANDOM
Rwork0.23898 ---
all0.24079 52185 --
obs0.23872 49551 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.46 Å2
Baniso -1Baniso -2Baniso -3
1-2.13 Å21.07 Å20 Å2
2--2.13 Å20 Å2
3----3.2 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9213 0 150 42 9405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0229613
X-RAY DIFFRACTIONr_angle_refined_deg2.361.97913068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7351156
X-RAY DIFFRACTIONr_chiral_restr0.1270.21447
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.027231
X-RAY DIFFRACTIONr_nbd_refined0.30.25033
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2403
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3060.2172
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2950.219
X-RAY DIFFRACTIONr_mcbond_it1.3371.55840
X-RAY DIFFRACTIONr_mcangle_it2.59729431
X-RAY DIFFRACTIONr_scbond_it4.62233773
X-RAY DIFFRACTIONr_scangle_it7.1884.53637
LS refinement shellResolution: 2.701→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.344 155
Rwork0.346 3013
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)
13.61271.5817-2.55652.7865-1.97165.44160.1357-0.195-0.1230.0378-0.2352-0.39110.12410.36230.09950.20220.0026-0.00930.08480.06970.2379110.48715.45956.774
25.00421.3491.47934.40910.01756.01530.150.0758-0.1317-0.1729-0.1328-0.6301-0.22780.5194-0.01720.2562-0.01380.13020.29870.12210.3363123.8429.3641.784
31.786-0.5093-0.4574.25142.33814.4894-0.10480.0722-0.20020.2085-0.04480.19530.2594-0.29840.14960.1754-0.0066-0.01980.0820.04480.183575.64213.58975.196
47.4778-0.1006-1.69153.8243-0.18113.1594-0.2412-0.36310.15110.38060.15920.1362-0.0166-0.10380.0820.33640.0266-0.04560.084-0.00050.170372.14533.82288.035
56.1830.69232.66791.57880.40743.196-0.00410.0157-0.3370.11970.1496-0.02670.29060.2196-0.14550.27720.00710.01410.025-0.07120.207179.3870.88738.199
61.6385-0.2576-0.10864.2520.99515.4461-0.1090.08640.0832-0.14640.0143-0.0585-0.0412-0.02350.09470.1858-0.0294-0.02640.1047-0.07360.270462.168.62822.625
75.5687-0.12051.65151.3526-0.03062.03450.1780.4709-0.439-0.385-0.12280.09480.27990.2265-0.05530.35980.01750.05290.3361-0.06690.244795.02529.8323.717
81.93660.49190.66610.65430.52272.7480.1811-0.0453-0.29590.1159-0.207-0.24920.56480.43770.02590.26360.04720.02410.43230.02090.2736113.62725.67919.721
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA43 - 21543 - 215
2X-RAY DIFFRACTION2AA227 - 345227 - 345
3X-RAY DIFFRACTION3BB44 - 21544 - 215
4X-RAY DIFFRACTION4BB227 - 345227 - 345
5X-RAY DIFFRACTION5CC41 - 21541 - 215
6X-RAY DIFFRACTION6CC227 - 357227 - 357
7X-RAY DIFFRACTION7DD43 - 21543 - 215
8X-RAY DIFFRACTION8DD224 - 342224 - 342
Refinement
*PLUS
Highest resolution: 2.7 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.274 / Rfactor Rwork: 0.239
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.36

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