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- PDB-8x5l: The Crystal Structure of PRKACA from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8x5l
TitleThe Crystal Structure of PRKACA from Biortus.
ComponentscAMP-dependent protein kinase catalytic subunit alpha
KeywordsTRANSFERASE / Serine/threonine-protein kinase / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / HDL assembly / mitochondrial protein catabolic process / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / regulation of protein binding / nucleotide-activated protein kinase complex / high-density lipoprotein particle assembly / Rap1 signalling ...PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / HDL assembly / mitochondrial protein catabolic process / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / regulation of protein binding / nucleotide-activated protein kinase complex / high-density lipoprotein particle assembly / Rap1 signalling / renal water homeostasis / regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cell communication by electrical coupling involved in cardiac conduction / cAMP-dependent protein kinase / cellular response to cold / Loss of phosphorylation of MECP2 at T308 / regulation of osteoblast differentiation / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / sperm capacitation / cAMP-dependent protein kinase activity / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / Triglyceride catabolism / protein kinase A regulatory subunit binding / plasma membrane raft / PKA activation in glucagon signalling / : / Regulation of MECP2 expression and activity / mesoderm formation / RET signaling / DARPP-32 events / Interleukin-3, Interleukin-5 and GM-CSF signaling / regulation of cardiac muscle contraction / regulation of cardiac conduction / sperm flagellum / regulation of macroautophagy / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Hedgehog 'off' state / negative regulation of smoothened signaling pathway / regulation of proteasomal protein catabolic process / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / positive regulation of gluconeogenesis / Recruitment of mitotic centrosome proteins and complexes / sperm midpiece / negative regulation of TORC1 signaling / Recruitment of NuMA to mitotic centrosomes / protein kinase A signaling / Mitochondrial protein degradation / calcium channel complex / Anchoring of the basal body to the plasma membrane / cellular response to epinephrine stimulus / regulation of cytosolic calcium ion concentration / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / regulation of heart rate / CD209 (DC-SIGN) signaling / AURKA Activation by TPX2 / FCGR3A-mediated IL10 synthesis / positive regulation of protein export from nucleus / acrosomal vesicle / neural tube closure / Regulation of insulin secretion / cellular response to glucose stimulus / Degradation of GLI1 by the proteasome / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / mRNA processing / cytokine-mediated signaling pathway / VEGFA-VEGFR2 Pathway / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / Regulation of PLK1 Activity at G2/M Transition / manganese ion binding / cellular response to heat / Factors involved in megakaryocyte development and platelet production / peptidyl-serine phosphorylation / dendritic spine / regulation of cell cycle / protein kinase activity / nuclear speck / mitochondrial matrix / protein domain specific binding / protein phosphorylation
Similarity search - Function
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. ...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
Chem-RKD / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Lin, D. / Pan, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of PRKACA from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Lin, D. / Pan, W.
History
DepositionNov 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cAMP-dependent protein kinase catalytic subunit alpha
B: cAMP-dependent protein kinase catalytic subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1605
Polymers81,5072
Non-polymers6533
Water46826
1
A: cAMP-dependent protein kinase catalytic subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0913
Polymers40,7541
Non-polymers3382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area16340 Å2
MethodPISA
2
B: cAMP-dependent protein kinase catalytic subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0682
Polymers40,7541
Non-polymers3151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.272, 77.272, 142.698
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLU / End label comp-ID: GLU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 17 - 333 / Label seq-ID: 18 - 334

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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


Mass: 40753.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKACA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P17612
#2: Chemical ChemComp-RKD / (2S)-2-(4-chlorophenyl)-2-hydroxy-2-[4-(1H-pyrazol-4-yl)phenyl]ethanaminium / (1S)-2-AMINO-1-(4-CHLOROPHENYL)-1-(4-(1H-PYRAZOL-4-YL)PHENYL)ETHAN-1-OL


Mass: 314.789 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H17ClN3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M NaAC, 0.1M Na3citrate pH5.5, 10% PEG 4000, 40% v/v Polypropylene glycol P 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97951 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.75→47.57 Å / Num. obs: 21778 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 0.999 / Net I/σ(I): 16.4
Reflection shellResolution: 2.75→2.9 Å / Num. unique obs: 3161 / CC1/2: 0.821

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→43.418 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / SU B: 14.235 / SU ML: 0.274 / Cross valid method: FREE R-VALUE / ESU R Free: 0.363
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2545 1132 5.207 %
Rwork0.2009 20609 -
all0.204 --
obs-21741 99.972 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 71.871 Å2
Baniso -1Baniso -2Baniso -3
1-0.965 Å2-0 Å2-0 Å2
2--0.965 Å2-0 Å2
3----1.93 Å2
Refinement stepCycle: LAST / Resolution: 2.75→43.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5266 0 45 26 5337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0125454
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165013
X-RAY DIFFRACTIONr_angle_refined_deg0.9471.657362
X-RAY DIFFRACTIONr_angle_other_deg0.3281.57211674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3245632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.778528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52710968
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.0610269
X-RAY DIFFRACTIONr_chiral_restr0.0480.2767
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026076
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021166
X-RAY DIFFRACTIONr_nbd_refined0.1990.21061
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.24812
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22702
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22811
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2128
X-RAY DIFFRACTIONr_metal_ion_refined0.0330.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.130.211
X-RAY DIFFRACTIONr_nbd_other0.1370.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.250.26
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0120.21
X-RAY DIFFRACTIONr_mcbond_it2.4757.292543
X-RAY DIFFRACTIONr_mcbond_other2.4757.292543
X-RAY DIFFRACTIONr_mcangle_it4.18110.9233170
X-RAY DIFFRACTIONr_mcangle_other4.18110.9253171
X-RAY DIFFRACTIONr_scbond_it2.2977.4812911
X-RAY DIFFRACTIONr_scbond_other2.2977.4812912
X-RAY DIFFRACTIONr_scangle_it3.9311.1324192
X-RAY DIFFRACTIONr_scangle_other3.92911.1324193
X-RAY DIFFRACTIONr_lrange_it6.78487.9586099
X-RAY DIFFRACTIONr_lrange_other6.78387.9536100
X-RAY DIFFRACTIONr_ncsr_local_group_10.1020.059888
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.10190.05009
12AX-RAY DIFFRACTIONLocal ncs0.10190.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.75-2.8210.377890.31514770.31915660.8960.9391000.299
2.821-2.8980.372760.30315050.30615810.9220.9471000.276
2.898-2.9820.354980.27214250.27715240.9210.95899.93440.246
2.982-3.0730.275940.26813630.26814570.9470.9591000.243
3.073-3.1730.268990.25713230.25814220.9470.9631000.233
3.173-3.2840.26570.24713210.24813780.9490.9651000.224
3.284-3.4070.302680.24812810.25113490.9420.9651000.228
3.407-3.5460.314660.23312120.23712780.9390.9691000.214
3.546-3.7020.239480.21511640.21612120.9660.9721000.196
3.702-3.8810.252690.20911330.21112020.960.9741000.194
3.881-4.090.26570.18410520.18811090.9630.9791000.174
4.09-4.3350.213460.1710210.17210670.9740.9831000.164
4.335-4.6310.207570.1559500.15810070.9770.9851000.152
4.631-4.9980.239520.1598770.1639290.9660.9851000.16
4.998-5.4670.248390.188260.1838650.9650.9841000.18
5.467-6.1010.278290.1847320.1877610.9590.9811000.178
6.101-7.0210.197260.1846800.1847060.9720.981000.184
7.021-8.5440.214260.1675680.1695940.9770.9841000.173
8.544-11.8550.236220.1384320.1424540.9710.9911000.154
11.855-43.4180.15140.1942670.1922810.9890.9741000.207

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