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- PDB-6y8c: Crystal structure of the cAMP-dependent protein kinase A cocrysta... -

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Basic information

Entry
Database: PDB / ID: 6y8c
TitleCrystal structure of the cAMP-dependent protein kinase A cocrystallized with ATP and PKI (5-24)
Components(cAMP-dependent protein kinase ...) x 2
KeywordsTRANSFERASE / phosphotransferase / signalling pathways / glycogen metabolism / serine/threonine kinase
Function / homology
Function and homology information


negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / negative regulation of protein import into nucleus ...negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / negative regulation of protein import into nucleus / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / mesoderm formation / sperm flagellum / plasma membrane raft / axoneme / postsynaptic modulation of chemical synaptic transmission / regulation of G2/M transition of mitotic cell cycle / negative regulation of TORC1 signaling / regulation of proteasomal protein catabolic process / positive regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / protein export from nucleus / acrosomal vesicle / positive regulation of protein export from nucleus / negative regulation of smoothened signaling pathway / neural tube closure / positive regulation of cholesterol biosynthetic process / cellular response to glucose stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / manganese ion binding / cellular response to heat / postsynapse / regulation of cell cycle / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / magnesium ion binding / mitochondrion / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / 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 ...cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / 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
ADENOSINE-5'-TRIPHOSPHATE / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsOebbeke, M. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: A crystallographic study of cAMP-dependent protein kinase A in complex with different Fasudil-derivatives
Authors: Oebbeke, M. / Wienen-Schmidt, B. / Gerber, H.-D. / Heine, A. / Klebe, G.
History
DepositionMar 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 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: cAMP-dependent protein kinase catalytic subunit alpha
B: cAMP-dependent protein kinase inhibitor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,41911
Polymers43,2602
Non-polymers1,1589
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-31 kcal/mol
Surface area15150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.980, 78.916, 88.388
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

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Components

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CAMP-dependent protein kinase ... , 2 types, 2 molecules AB

#1: Protein cAMP-dependent protein kinase catalytic subunit alpha / PKA C-alpha


Mass: 41033.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: PRKACA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25321, cAMP-dependent protein kinase
#2: Protein/peptide cAMP-dependent protein kinase inhibitor alpha / PKI-alpha / cAMP-dependent protein kinase inhibitor / muscle/brain isoform


Mass: 2226.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P63248

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Non-polymers , 5 types, 309 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.72 Å3/Da / Density % sol: 54.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 30 mM MES-BIS-Tris-Buffer, 1 mM dithiothreitol, 0.1 mM sodium EDTA, LiCl, Mega 8, ATP MgCl2 and 18-23 % methanol (v/v), 0.7 mM PKI(5-24), 0.004 mL drop volume, 0.5 mL reservoir volume

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.76→44.194 Å / Num. obs: 44973 / % possible obs: 99.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 19.59 Å2 / Rsym value: 0.071 / Net I/σ(I): 18.92
Reflection shellResolution: 1.76→1.87 Å / Mean I/σ(I) obs: 3.67 / Num. unique obs: 7061 / Rsym value: 0.059

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHASERphasing
Cootmodel building
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F14

6f14


Resolution: 1.76→43.32 Å / SU ML: 0.1565 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.4021
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1902 2249 5 %
Rwork0.1609 42723 -
obs0.1623 44972 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.43 Å2
Refinement stepCycle: LAST / Resolution: 1.76→43.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2846 0 64 300 3210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583047
X-RAY DIFFRACTIONf_angle_d0.86194141
X-RAY DIFFRACTIONf_chiral_restr0.054440
X-RAY DIFFRACTIONf_plane_restr0.0053527
X-RAY DIFFRACTIONf_dihedral_angle_d17.72621778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.80.23911340.19472553X-RAY DIFFRACTION96.93
1.8-1.840.24011380.18952616X-RAY DIFFRACTION99.42
1.84-1.880.25021400.17592656X-RAY DIFFRACTION99.54
1.88-1.940.18921370.16122613X-RAY DIFFRACTION99.64
1.94-1.990.19221390.16492639X-RAY DIFFRACTION99.68
1.99-2.060.18831400.15922650X-RAY DIFFRACTION99.75
2.06-2.130.19061400.15082666X-RAY DIFFRACTION99.75
2.13-2.220.20871390.14812637X-RAY DIFFRACTION99.57
2.22-2.320.18281390.14352653X-RAY DIFFRACTION99.89
2.32-2.440.19871410.15562667X-RAY DIFFRACTION99.93
2.44-2.590.20761400.15682673X-RAY DIFFRACTION99.93
2.59-2.790.1941420.1642686X-RAY DIFFRACTION99.96
2.79-3.070.17731410.15862689X-RAY DIFFRACTION99.96
3.07-3.520.19011430.16272719X-RAY DIFFRACTION99.93
3.52-4.430.16271450.14412741X-RAY DIFFRACTION99.97
4.43-43.320.18641510.18052865X-RAY DIFFRACTION99.97
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)
10.75508682799-0.01798051233020.3259170224140.8917267932940.007281280373940.3245925803580.005846588470990.132580724628-0.0189808308579-0.06759589477160.000659093933556-0.123075933349-0.006656489885790.118220732315-0.0001643083494990.13183489150.001544150539340.01273834411240.162429567725-0.003676495133120.15197263195519.4107245206-15.8736004595-17.7716156168
20.4188451361370.1881537027660.1362732118620.3089228898710.02238252699920.115955164432-0.01641702105950.0640089412767-0.0214098051062-0.01484007010370.0135381809777-0.02863093188160.03707452879460.02288338579932.54612506747E-50.1231563617550.01207195363170.008830425679230.105725235419-0.005665757739070.1108526754035.99672094049-20.3909960448-13.6723237983
30.6073624940040.44684566324-0.08236811905420.696727954682-0.1757471752740.149773681614-0.02257507356360.05466803503070.122182163427-0.05893084524510.01847876384880.1441921237060.0395435340679-0.07714880987340.0001937853408650.08639088970050.003520431221530.001483919293880.0916617652135-0.004133410391350.100501226136-9.40909044175-19.9493945999-14.3774883605
40.924860553176-0.107113400030.08996793761830.3656019723330.3249034817910.2801837189-0.02533397098650.11468570495-0.138622919504-0.06474740672390.0129317561514-0.02085684622250.09260447579140.02069067899130.01047817035310.1416024650290.007396648276980.0132662119510.124203480922-0.0324852405390.13429288248715.7653054378-24.5368581678-16.0458546716
50.0128740683145-0.00710371625548-0.01285881769130.0175718430906-0.01895490943890.0397958914904-0.015421746775-0.13810175310.233337057318-0.003125662806310.003524029659850.1958101050480.1895459247130.218013659549-0.001771493527040.1844926268180.001764110901990.001001803392040.152472844277-0.04065849360910.178858381808-9.90981438912-38.0299645011-21.6993557308
60.1329729259550.0588535788194-0.0719736467490.181544164449-0.207667065720.300885768341-0.03140622789880.04356125641080.151105509184-0.1247512603440.200085334687-0.310437819618-0.2333218314690.1507593047930.03760288805440.223605031074-0.03136498689630.02157005380790.178018628193-0.04264229458760.198841598162-0.089493478636-29.6285117352-26.5457086739
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 114 )
2X-RAY DIFFRACTION2chain 'A' and (resid 115 through 198 )
3X-RAY DIFFRACTION3chain 'A' and (resid 199 through 297 )
4X-RAY DIFFRACTION4chain 'A' and (resid 298 through 350 )
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 11 )
6X-RAY DIFFRACTION6chain 'B' and (resid 12 through 22 )

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