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- PDB-4wih: Crystal structure of cAMP-dependent Protein Kinase A from Cricetu... -

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Basic information

Entry
Database: PDB / ID: 4wih
TitleCrystal structure of cAMP-dependent Protein Kinase A from Cricetulus griseus
Components
  • cAMP Dependent Protein Kinase Inhibitor PKI-tide
  • cAMP-dependent protein kinase catalytic subunit alphaCAMP-dependent pathway
KeywordsTRANSFERASE / PKA / Kinase / Serine/threonine-protein kinase / ATP-binding / cAMP / Nucleotide-binding
Function / homology
Function and homology information


regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / sperm capacitation / regulation of osteoblast differentiation / cAMP-dependent protein kinase activity ...regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / sperm capacitation / regulation of osteoblast differentiation / cAMP-dependent protein kinase activity / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / axoneme / plasma membrane raft / mesoderm formation / sperm flagellum / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / positive regulation of gluconeogenesis / negative regulation of TORC1 signaling / protein export from nucleus / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / positive regulation of protein export from nucleus / neural tube closure / cellular response to glucose stimulus / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / mRNA processing / cellular response to heat / manganese ion binding / dendritic spine / regulation of cell cycle / nuclear speck / protein domain specific binding / phosphorylation / protein serine kinase activity / centrosome / protein serine/threonine kinase activity / glutamatergic synapse / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / 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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...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. / 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
cAMP-dependent protein kinase inhibitor alpha / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.139 Å
AuthorsKudlinzki, D. / Linhard, V.L. / Saxena, K. / Dreyer, M. / Schwalbe, H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: High-resolution crystal structure of cAMP-dependent protein kinase from Cricetulus griseus.
Authors: Kudlinzki, D. / Linhard, V.L. / Saxena, K. / Sreeramulu, S. / Gande, S. / Schieborr, U. / Dreyer, M. / Schwalbe, H.
History
DepositionSep 25, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Aug 19, 2015Group: Database references
Revision 1.4Jan 10, 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

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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 PKI-tide


Theoretical massNumber of molelcules
Total (without water)43,1072
Polymers43,1072
Non-polymers00
Water10,539585
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-0 kcal/mol
Surface area17780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.276, 72.949, 109.351
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 41113.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Phosphorylation of S11, T198, S339 / Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: PRKACA / Production host: Escherichia coli (E. coli) / References: UniProt: P25321, cAMP-dependent protein kinase
#2: Protein/peptide cAMP Dependent Protein Kinase Inhibitor PKI-tide


Mass: 1993.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Sigma-Aldrich product no. SCP0064 / Source: (synth.) synthetic construct (others) / References: UniProt: G3HK48*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 585 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: Reservoir: 20-25% Methanol Drop: 25mM MesBisTris buffer pH6.5, 50mM LiCl, 1mM PKI, 0.35mM PKA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.139→45.53 Å / Num. obs: 169712 / % possible obs: 99.7 % / Redundancy: 6.49 % / Rsym value: 0.05 / Net I/σ(I): 17.59
Reflection shellResolution: 1.139→1.21 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.32 / % possible all: 98.7

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Processing

Software
NameVersionClassification
XDS(xdsapp 1.02)data reduction
Aimlessdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YDS

1yds


Resolution: 1.139→39.874 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 17.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1914 8485 5 %
Rwork0.1773 --
obs0.178 169709 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.139→39.874 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3013 0 0 585 3598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063176
X-RAY DIFFRACTIONf_angle_d1.0134295
X-RAY DIFFRACTIONf_dihedral_angle_d14.7431197
X-RAY DIFFRACTIONf_chiral_restr0.042446
X-RAY DIFFRACTIONf_plane_restr0.005554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1391-1.1520.26332650.2515043X-RAY DIFFRACTION96
1.152-1.16560.26062810.24195334X-RAY DIFFRACTION99
1.1656-1.17980.23172780.2395288X-RAY DIFFRACTION99
1.1798-1.19470.24452800.23215321X-RAY DIFFRACTION100
1.1947-1.21040.23372810.22435332X-RAY DIFFRACTION100
1.2104-1.2270.2452800.22045318X-RAY DIFFRACTION100
1.227-1.24450.22972800.21335315X-RAY DIFFRACTION100
1.2445-1.26310.24092820.20895356X-RAY DIFFRACTION100
1.2631-1.28290.20752790.20495298X-RAY DIFFRACTION100
1.2829-1.30390.21242810.20395343X-RAY DIFFRACTION100
1.3039-1.32640.20912810.20385343X-RAY DIFFRACTION100
1.3264-1.35050.1842830.19975372X-RAY DIFFRACTION100
1.3505-1.37650.19922800.1885336X-RAY DIFFRACTION100
1.3765-1.40460.18622830.19345366X-RAY DIFFRACTION100
1.4046-1.43510.20062810.1945348X-RAY DIFFRACTION100
1.4351-1.46850.20512840.19235381X-RAY DIFFRACTION100
1.4685-1.50520.19482810.18115352X-RAY DIFFRACTION100
1.5052-1.54590.1972840.17545395X-RAY DIFFRACTION100
1.5459-1.59140.19892820.185353X-RAY DIFFRACTION100
1.5914-1.64280.20292840.17445390X-RAY DIFFRACTION100
1.6428-1.70150.1962830.17395392X-RAY DIFFRACTION100
1.7015-1.76960.18182850.17245409X-RAY DIFFRACTION100
1.7696-1.85020.18092820.17625364X-RAY DIFFRACTION100
1.8502-1.94770.19742860.18085427X-RAY DIFFRACTION100
1.9477-2.06970.18152850.18195420X-RAY DIFFRACTION100
2.0697-2.22950.19012860.17485434X-RAY DIFFRACTION100
2.2295-2.45390.16962880.17495457X-RAY DIFFRACTION100
2.4539-2.80890.20392890.17665493X-RAY DIFFRACTION100
2.8089-3.53850.1882900.16635507X-RAY DIFFRACTION100
3.5385-39.8980.16953010.15055737X-RAY DIFFRACTION100
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
14.851-1.07082.83822.1128-0.50975.94420.05060.2413-0.0709-0.1001-0.1250.00750.31130.04970.0420.13740.02560.05130.15090.0060.17Chain A catalytic domain9.6518.40812.1909
20.3478-0.63210.15151.6217-0.4950.19680.3296-0.2736-0.51330.45880.019-0.73810.12730.29940.0330.23050.0634-0.22440.3949-0.13410.6059Chain A catalytic domain24.541523.205230.3396
31.48140.13880.28052.60930.41881.93610.087-0.5769-0.0830.74720.0094-0.30150.2624-0.1934-0.05140.28650.0057-0.10370.340.01860.1888Chain A catalytic domain15.189914.026631.8692
40.65090.2005-0.4221.68520.48320.65510.0313-0.13190.05130.1330.0531-0.3262-0.00340.1692-0.00910.08140.0021-0.02330.1099-0.01960.1059Chain A catalytic domain10.813422.750118.7539
50.7528-0.032-0.07592.1569-0.34610.7557-0.0127-0.1169-0.03120.1360.02660.06190.01670.0155-0.00710.0930.00020.0030.0903-0.00340.0721Chain A catalytic domain-0.996617.443222.6597
62.7936-0.48990.99185.9167-0.24463.08150.00330.03460.01870.055-0.01920.4994-0.0704-0.2850.01710.07580.0159-0.010.1279-0.00510.1316Chain A catalytic domain-13.119324.796711.6885
72.83290.4057-0.71591.4728-0.23661.81270.01720.1835-0.0815-0.1675-0.0036-0.01350.0255-0.0779-0.00320.11730.016-0.00890.0831-0.01430.0857Chain A catalytic domain-0.038918.74816.3087
82.2085-1.22571.13534.8801-1.65192.11310.2955-0.5556-0.14120.76230.008-0.32950.0430.05450.07470.3381-0.0432-0.2010.3808-0.04160.331Chain A catalytic domain18.754623.821635.1565
93.9430.6974-0.88276.3118-0.44843.94950.1023-0.3103-0.14240.3917-0.0430.32640.2659-0.2559-0.01080.2081-0.03270.00150.1418-0.00520.108Chain A Inhibitor Peptide-3.463724.364231.5258
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 68 )
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 98 )
4X-RAY DIFFRACTION4chain 'A' and (resid 99 through 161 )
5X-RAY DIFFRACTION5chain 'A' and (resid 162 through 253 )
6X-RAY DIFFRACTION6chain 'A' and (resid 254 through 273 )
7X-RAY DIFFRACTION7chain 'A' and (resid 274 through 317 )
8X-RAY DIFFRACTION8chain 'A' and (resid 318 through 351 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 15 )

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