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- PDB-8ukp: cAMP-dependent protein kinase A catalytic domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 8ukp
TitlecAMP-dependent protein kinase A catalytic domain in complex with voltage gated calcium channel peptide ternary complex 1
Components
  • ARG-GLY-PHE-LEU-ARG-SER-ALA-SER-LEU-GLY-ARG-ARG-ALA-SER-PHE-HIS-LEU
  • cAMP-dependent protein kinase catalytic subunit alpha
KeywordsTRANSFERASE / Protein Kinase / Complex / Ion Channel / Voltage gated calcium channel / Cardiac channel / Stress signaling
Function / homology
Function and homology information


PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Regulation of insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / GPER1 signaling / Hedgehog 'off' state ...PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Regulation of insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / GPER1 signaling / Hedgehog 'off' state / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / AURKA Activation by TPX2 / Factors involved in megakaryocyte development and platelet production / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Regulation of PLK1 Activity at G2/M Transition / Interleukin-3, Interleukin-5 and GM-CSF signaling / CD209 (DC-SIGN) signaling / RET signaling / Mitochondrial protein degradation / Ion homeostasis / VEGFA-VEGFR2 Pathway / 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 / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / protein kinase A regulatory subunit binding / mesoderm formation / cAMP/PKA signal transduction / sperm flagellum / plasma membrane raft / axoneme / postsynaptic modulation of chemical synaptic transmission / negative regulation of TORC1 signaling / regulation of proteasomal protein catabolic process / sperm midpiece / 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 / modulation of chemical synaptic transmission / 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 / peptidyl-serine phosphorylation / manganese ion binding / cellular response to heat / postsynapse / protein kinase activity / 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 / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsHaji-Ghassemi, O. / Van Petegem, F.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-153305 Canada
Canada Foundation for Innovation Canada
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Crystallographic, kinetic, and calorimetric investigation of PKA interactions with L-type calcium channels and Rad GTPase.
Authors: Yoo, R. / Haji-Ghassemi, O. / Bader, M. / Xu, J. / McFarlane, C. / Van Petegem, F.
History
DepositionOct 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2025Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: ARG-GLY-PHE-LEU-ARG-SER-ALA-SER-LEU-GLY-ARG-ARG-ALA-SER-PHE-HIS-LEU
E: cAMP-dependent protein kinase catalytic subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0895
Polymers41,5342
Non-polymers5553
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-21 kcal/mol
Surface area15190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.630, 118.630, 57.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein/peptide ARG-GLY-PHE-LEU-ARG-SER-ALA-SER-LEU-GLY-ARG-ARG-ALA-SER-PHE-HIS-LEU


Mass: 1936.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Protein cAMP-dependent protein kinase catalytic subunit alpha / PKA C-alpha


Mass: 39598.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prkaca, Pkaca / Production host: Escherichia coli (E. coli) / References: UniProt: P05132, cAMP-dependent protein kinase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 53.1 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M HEPES pH 7.0, 18% w/v PEG 12K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.85→35 Å / Num. obs: 9956 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.028 / Rrim(I) all: 0.102 / Χ2: 0.928 / Net I/σ(I): 7.6 / Num. measured all: 135235
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.85-2.9214.14.0036330.5710.8531.0934.1530.862100
2.92-2.9913.82.4616550.6850.9020.6842.5560.844100
2.99-3.0713.52.1816400.7520.9270.612.2660.892100
3.07-3.1612.31.3566560.8590.9610.4011.4150.918100
3.16-3.2614.60.8836320.9370.9840.2380.9150.933100
3.26-3.3814.60.6236690.9570.9890.1680.6460.923100
3.38-3.5114.50.4066390.9840.9960.110.4210.958100
3.51-3.6714.20.2576590.9930.9980.070.2670.968100
3.67-3.8714.10.1746580.9940.9980.0480.180.984100
3.87-4.1112.70.1246680.9960.9990.0360.1291.057100
4.11-4.43140.0826670.9970.9990.0230.0851100
4.43-4.8714.10.0656570.9980.9990.0180.0670.912100
4.87-5.5713.60.0526740.99910.0150.0540.898100
5.57-7.0112.40.0456960.99910.0130.0470.886100
7.01-3511.70.0297530.99810.0090.0310.88599.9

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Processing

Software
NameVersionClassification
PHENIX1.20rc1_4392refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→33.8 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2807 467 5.07 %
Rwork0.2396 --
obs0.2418 9212 92.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→33.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2671 0 33 12 2716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022773
X-RAY DIFFRACTIONf_angle_d0.4753770
X-RAY DIFFRACTIONf_dihedral_angle_d13.953964
X-RAY DIFFRACTIONf_chiral_restr0.039412
X-RAY DIFFRACTIONf_plane_restr0.004473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.260.3011300.30742354X-RAY DIFFRACTION77
3.26-4.110.3161710.25323123X-RAY DIFFRACTION100
4.11-33.80.25171660.21263268X-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)Origin x (Å)Origin y (Å)Origin z (Å)
10.0068-0.0073-0.00190.008-0.00620.01960.00560.0119-0.0179-0.0330.0290.04480.0175-0.02540.01470.18720.0057-0.05440.2705-0.18960.372-2.5546.611-12.458
20.00170.00490.00270.00590.00380.00250.0079-0.00290.00450.0042-0.0304-0.0070.03120.036-00.7008-0.0814-0.08430.4731-0.11560.6664-1.52610.819-8.401
3-0.00020.0007-0.00010.00230.00010.0027-0.0255-0.0031-0.04490.0168-0.0101-0.0022-0.01610.008100.7367-0.09550.07580.6212-0.00350.4811-8.36525.70314.307
40.00090.0005-0.0009-0.0005-0.00040.0009-0.00160.00540.0036-0.00370.0048-0.0004-0.0022-0.0151-00.7703-0.0748-0.03050.8842-0.12240.85-8.62234.1074.699
5-0.00060.00010.00020.00010.00030.0003-0.012-0.0092-0.0037-0.00660.00860.0001-0.00160.008500.88430.0242-0.08750.7932-0.04290.6819-0.53723.0213.893
60.0015-0.0001-0.00080.0001-0.00030.0010.006-0.01630.00810.0050.00790.016-0.0050.0144-00.7552-0.0567-0.05780.7503-0.01850.5948-13.31628.7183.143
70.0001-0.0001-0.0002-0.00020.00080.0090.0037-0.00470.00250.00390.0032-0.00140.005-0.00401.06570.0628-0.04451.1853-0.00091.1026-21.5931.671-4.641
80.0006-0.00080.00020.0026-0.000500.01070.00970.00430.00220.0059-0.0089-0.00250.00300.51770.0024-0.0420.6462-0.19650.6288-15.06725.981-9.478
90.00550.0009-0.00560.00320.00230.0002-0.0282-0.0634-0.01810.0971-0.0557-0.02750.0366-0.0719-0.0010.4209-0.138-0.26130.4527-0.09020.458-3.31919.837-1.808
100.0020.00390.0019-0.00160.00090.0008-0.01770.0074-0.02460.0111-0.0340.0135-0.02850.004200.7379-0.0794-0.04590.762-0.13230.5654-9.22825.3064.868
110.03020.02660.03140.02670.0006-0.01460.2588-0.095-0.26110.00820.0523-0.01580.16590.15870.1663-1.1187-0.0135-1.48060.1016-0.0402-0.68178.06732.136-8.102
120.00480.00370.0090.00730.00170.00190.03660.0186-0.0487-0.0814-0.05980.08050.0377-0.0154-0.01590.2387-0.0715-0.5560.2983-0.20160.2507-7.53727.349-17.08
130.002-0.00370.00390.00070.00160.0020.01030.02850.0149-0.0445-0.00110.04340.0160.00170.00950.17960.0214-0.38270.1627-0.19720.0633-4.02237.138-23.233
140.105-0.04570.04880.034-0.03230.03320.07880.0421-0.0406-0.1022-0.00750.02320.0607-0.01240.0221-0.01720.0442-0.3969-0.1045-0.3034-0.07594.66233.747-19.301
150.0191-0.00830.0231-0.0019-0.00030.01840.02740.02710.0486-0.08820.0476-0.00520.0120.01930.0390.0241-0.0234-0.39440.1111-0.2529-0.07760.1146.8-22.114
160.00250.0022-0.01090.00120.00170.00960.02390.0156-0.0242-0.0787-0.01080.0123-0.03050.06180.01330.12240.25440.19460.3193-0.4127-0.058513.48639.511-24.649
170.0079-0.002-0.010.0157-0.00310.019-0.0257-0.0438-0.1027-0.1159-0.042-0.11960.01330.0377-0.03810.28690.4951-0.13730.1408-0.34380.453514.57625.698-21.429
180.00580.00050.00630.00140.00060.0026-0.0181-0.01430.01970.0128-0.031200.00960.0189-00.3219-0.0043-0.39020.48310.0380.576517.1427.118-2.014
1900.00070.0002-0.00010.0001-0.00010.005-0.0046-0.0151-0.00350.00730.0111-0.001-0.0003-01.028-0.0176-0.04761.03850.00721.01358.16536.47410.723
200.01190.0062-0.00290.00450.00430.0025-0.0250.00290.00110.02350.0029-0.0012-0.02170.001101.0259-0.01910.02341.0148-0.0731.0039-9.28334.3027.04
210.0076-0.0017-0.00060.00210.00190.00110.0044-0.00790-0.00240.0001-0.0132-0.0005-0.003201.1522-0.1126-0.08551.2601-0.0961.2869-21.59419.898-1.372
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 1969:1984 )C1969 - 1984
2X-RAY DIFFRACTION2( CHAIN E AND RESID 17:38 )E17 - 38
3X-RAY DIFFRACTION3( CHAIN E AND RESID 39:48 )E39 - 48
4X-RAY DIFFRACTION4( CHAIN E AND RESID 49:61 )E49 - 61
5X-RAY DIFFRACTION5( CHAIN E AND RESID 62:71 )E62 - 71
6X-RAY DIFFRACTION6( CHAIN E AND RESID 72:77 )E72 - 77
7X-RAY DIFFRACTION7( CHAIN E AND RESID 78:83 )E78 - 83
8X-RAY DIFFRACTION8( CHAIN E AND RESID 84:91 )E84 - 91
9X-RAY DIFFRACTION9( CHAIN E AND RESID 92:113 )E92 - 113
10X-RAY DIFFRACTION10( CHAIN E AND RESID 114:123 )E114 - 123
11X-RAY DIFFRACTION11( CHAIN E AND RESID 124:183 )E124 - 183
12X-RAY DIFFRACTION12( CHAIN E AND RESID 184:202 )E184 - 202
13X-RAY DIFFRACTION13( CHAIN E AND RESID 203:214 )E203 - 214
14X-RAY DIFFRACTION14( CHAIN E AND RESID 215:233 )E215 - 233
15X-RAY DIFFRACTION15( CHAIN E AND RESID 234:254 )E234 - 254
16X-RAY DIFFRACTION16( CHAIN E AND RESID 255:277 )E255 - 277
17X-RAY DIFFRACTION17( CHAIN E AND RESID 278:306 )E278 - 306
18X-RAY DIFFRACTION18( CHAIN E AND RESID 307:317 )E307 - 317
19X-RAY DIFFRACTION19( CHAIN E AND RESID 318:326 )E318 - 326
20X-RAY DIFFRACTION20( CHAIN E AND RESID 327:341 )E327 - 341
21X-RAY DIFFRACTION21( CHAIN E AND RESID 342:350 )E342 - 350

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