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- PDB-5jr7: Crystal structure of an ACRDYS heterodimer [RIa(92-365):C] of PKA -

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Basic information

Entry
Database: PDB / ID: 5jr7
TitleCrystal structure of an ACRDYS heterodimer [RIa(92-365):C] of PKA
Components
  • cAMP-dependent protein kinase catalytic subunit alpha
  • cAMP-dependent protein kinase type I-alpha regulatory subunit
KeywordsTransferase/cAMP binding Protein / PKA signaling / RIa subunit / disease mutations / dysfunctional ACRDYS mutant / Transferase-cAMP binding Protein complex
Function / homology
Function and homology information


spontaneous exocytosis of neurotransmitter / negative regulation of meiotic cell cycle / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / HDL assembly / regulation of protein processing / DARPP-32 events / Rap1 signalling / PKA activation / Regulation of insulin secretion ...spontaneous exocytosis of neurotransmitter / negative regulation of meiotic cell cycle / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / HDL assembly / regulation of protein processing / DARPP-32 events / Rap1 signalling / PKA activation / Regulation of insulin secretion / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Vasopressin regulates renal water homeostasis via Aquaporins / Factors involved in megakaryocyte development and platelet production / cellular response to parathyroid hormone stimulus / GPER1 signaling / protein localization to lipid droplet / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Factors involved in megakaryocyte development and platelet production / PKA activation / Hedgehog 'off' state / Hedgehog 'off' state / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / regulation of cellular respiration / Interleukin-3, Interleukin-5 and GM-CSF signaling / Recruitment of NuMA to mitotic centrosomes / CD209 (DC-SIGN) signaling / AURKA Activation by TPX2 / MAPK6/MAPK4 signaling / RET signaling / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / cAMP-dependent protein kinase regulator activity / insulin secretion involved in cellular response to glucose stimulus / GLI3 is processed to GLI3R by the proteasome / sperm head-tail coupling apparatus / Regulation of PLK1 Activity at G2/M Transition / Mitochondrial protein degradation / cellular response to cold / VEGFA-VEGFR2 Pathway / nucleotide-activated protein kinase complex / interleukin-2-mediated signaling pathway / Ion homeostasis / mesoderm formation / cAMP-dependent protein kinase inhibitor activity / TORC1 signaling / potassium channel inhibitor activity / histone H1-4S35 kinase activity / cAMP-dependent protein kinase / positive regulation of triglyceride catabolic process / negative regulation of activated T cell proliferation / cAMP-dependent protein kinase activity / regulation of bicellular tight junction assembly / cAMP-dependent protein kinase complex / negative regulation of glycolytic process through fructose-6-phosphate / neural tube closure / negative regulation of glycolytic process / regulation of osteoblast differentiation / sperm capacitation / peptidyl-threonine phosphorylation / protein kinase A regulatory subunit binding / ciliary base / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / protein kinase A catalytic subunit binding / intracellular potassium ion homeostasis / immunological synapse / plasma membrane raft / cAMP binding / axoneme / cAMP/PKA signal transduction / postsynaptic modulation of chemical synaptic transmission / sperm flagellum / negative regulation of cAMP/PKA signal transduction / multivesicular body / regulation of synaptic transmission, glutamatergic / cellular response to nutrient levels / positive regulation of gluconeogenesis / positive regulation of protein export from nucleus / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / positive regulation of phagocytosis / negative regulation of TORC1 signaling / sperm midpiece / negative regulation of smoothened signaling pathway / acrosomal vesicle / regulation of proteasomal protein catabolic process / negative regulation of protein localization to chromatin / lipid droplet / cellular response to glucose stimulus / neuromuscular junction / positive regulation of protein localization to plasma membrane / regulation of microtubule cytoskeleton organization / positive regulation of cholesterol biosynthetic process / mRNA processing / peptidyl-serine phosphorylation
Similarity search - Function
cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : / Cyclic nucleotide-binding domain signature 2. / cAMP-dependent protein kinase catalytic subunit / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain ...cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : / Cyclic nucleotide-binding domain signature 2. / cAMP-dependent protein kinase catalytic subunit / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Jelly Rolls / Cyclic nucleotide-binding domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Jelly Rolls / 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 / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / cAMP-dependent protein kinase type I-alpha regulatory subunit / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.56 Å
AuthorsBruystens, J.G.H. / Wu, J. / Taylor, S.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 034921 United States
CitationJournal: J. Mol. Biol. / Year: 2016
Title: Structure of a PKA RI alpha Recurrent Acrodysostosis Mutant Explains Defective cAMP-Dependent Activation.
Authors: Bruystens, J.G. / Wu, J. / Fortezzo, A. / Del Rio, J. / Nielsen, C. / Blumenthal, D.K. / Rock, R. / Stefan, E. / Taylor, S.S.
History
DepositionMay 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 type I-alpha regulatory subunit
C: cAMP-dependent protein kinase catalytic subunit alpha
D: cAMP-dependent protein kinase type I-alpha regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,1556
Polymers143,3014
Non-polymers8542
Water00
1
A: cAMP-dependent protein kinase catalytic subunit alpha
B: cAMP-dependent protein kinase type I-alpha regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0783
Polymers71,6502
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-22 kcal/mol
Surface area27630 Å2
MethodPISA
2
C: cAMP-dependent protein kinase catalytic subunit alpha
D: cAMP-dependent protein kinase type I-alpha regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0783
Polymers71,6502
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-21 kcal/mol
Surface area28520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.146, 66.790, 87.932
Angle α, β, γ (deg.)101.76, 89.37, 105.27
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 40737.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prkaca, Pkaca / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P05132, cAMP-dependent protein kinase
#2: Protein cAMP-dependent protein kinase type I-alpha regulatory subunit


Mass: 30913.094 Da / Num. of mol.: 2 / Fragment: UNP residues 92-366
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: PRKAR1A / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P00514
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
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: 2.33 Å3/Da / Density % sol: 47.13 % / Description: There are two molecules per asymmetrical unit
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium thiocyanate and 20% PEG 3350 with the protein at a final concentration of 5 mg/ml in a 1.6 ul drop

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2014
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.56→50 Å / Num. obs: 15767 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.155 / Rsym value: 0.107 / Net I/σ(I): 11.8
Reflection shellResolution: 3.56→3.63 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.1 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.7_650refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QCS

2qcs


Resolution: 3.56→49.11 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 38.87
RfactorNum. reflection% reflectionSelection details
Rfree0.322 765 5.09 %Random selection
Rwork0.266 ---
obs0.269 15043 97.4 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Bsol: 74.42 Å2 / ksol: 0.29 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7709 Å20.1923 Å2-5.506 Å2
2--9.7992 Å2-8.1156 Å2
3----7.0283 Å2
Refinement stepCycle: LAST / Resolution: 3.56→49.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9611 0 54 0 9665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099971
X-RAY DIFFRACTIONf_angle_d1.73813489
X-RAY DIFFRACTIONf_dihedral_angle_d18.063690
X-RAY DIFFRACTIONf_chiral_restr0.1261452
X-RAY DIFFRACTIONf_plane_restr0.0071728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5601-3.83490.40171450.36682831X-RAY DIFFRACTION97
3.8349-4.22060.39021320.30442814X-RAY DIFFRACTION95
4.2206-4.83090.36361590.24722841X-RAY DIFFRACTION97
4.8309-6.08460.30651650.27292890X-RAY DIFFRACTION99
6.0846-49.11040.25581640.21822902X-RAY DIFFRACTION99
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)
10.44740.67580.27911.08340.42730.1717-0.13120.15170.0424-0.2797-0.09961.0231-0.72870.202-0.24641.03760.3876-0.52770.7090.03860.74143.9034-27.68777.3914
20.89130.2773-0.50172.1089-1.27961.53910.21590.37620.04120.11670.63531.1316-0.4117-0.77221.2926-0.1526-0.2077-0.06790.1565-0.0660.10946.5287-34.008122.8319
31.6014-0.1732-0.26070.5674-0.00830.4822-0.4420.45850.0280.0860.22580.1113-0.03620.011-0.69030.02620.059-0.02210.0763-0.0160.278424.1035-29.216224.2045
40.5038-0.2816-0.13620.16530.12410.37820.20680.50730.214-0.3566-0.188-0.0173-0.0624-0.03680.04360.2958-0.0460.03420.49970.0018-0.138326.8355-36.891511.6878
50.84190.3994-0.14750.427-0.36580.68210.13510.59490.7383-0.2215-0.10080.4572-0.4587-0.6267-0.35610.51010.3463-0.06061.0478-0.05490.8655-2.1268-32.09130.4277
60.3378-0.00930.00730.98950.58290.80940.0755-0.12330.11770.56750.27950.09630.2427-0.2493-0.39180.10150.4872-0.21050.22250.13890.741518.0362-9.950531.1525
70.0346-0.01460.05330.0087-0.01890.2104-0.16770.323-0.1030.02970.2109-0.25830.36060.5006-0.00990.469-0.07760.05650.2896-0.18550.931933.6984-4.062535.8501
80.72460.1483-0.20650.0936-0.18250.4487-0.1104-0.4721-0.25610.2042-0.0602-0.0402-0.1240.0212-0.4671.76420.2687-0.30050.35640.4760.077823.2745-11.457551.5686
90.054-0.0428-0.01840.0642-0.00790.03-0.0237-0.1027-0.01370.02660.02730.06330.05270.0536-0.04181.15290.21790.06330.1308-0.09740.486719.9886-16.360340.21
100.0691-0.0263-0.07650.07990.12680.2341-0.0008-0.1313-0.07820.32740.1999-0.07590.1930.16630.14651.36890.27750.28230.5323-0.10690.388324.3038-6.079951.3862
110.2014-0.1194-0.00110.27490.25420.3243-0.2733-0.05050.13830.2806-0.15260.3860.1285-0.0981-1.02620.7085-0.0907-0.0126-0.5967-0.27590.309326.083-4.096619.2413
120.4575-0.0706-0.31920.5720.03250.27260.07680.29490.1851-0.0167-0.03420.2377-0.0264-0.42420.08770.1157-0.2348-0.14480.22590.03570.622541.8508-4.747611.1379
130.01130.00120.02360.00080.00360.0476-0.04070.0240.058-0.0038-0.0386-0.0301-0.08280.0829-0.08291.1608-0.34730.27590.77670.25930.999564.92953.57076.1012
140.67080.34020.22950.6493-0.32610.916-0.0962-0.2577-0.0732-0.2652-0.0601-0.18140.13310.4839-1.41280.3541-0.22250.130.54960.00570.146645.5217-4.73728.9958
150.20290.22990.00460.64670.22210.1262-0.1441-0.0546-0.5064-0.1-0.2291-0.97230.64110.07960.0411.30160.14460.39490.79780.37630.91812.0725-26.059952.3278
160.3565-0.10230.18620.43430.23550.52940.25950.4534-0.1161-0.4964-0.0446-0.93690.46081.21380.0695-0.3634-0.03780.36090.36030.17640.41119.8039-26.227369.2516
170.4904-0.18130.53130.6809-0.60670.85640.38470.39330.4649-0.6786-0.46170.25840.45850.6875-0.12120.3038-0.11260.1061-0.47250.36380.0854-7.7009-31.232868.7736
180.2138-0.0689-0.17070.5275-0.29190.41430.24640.35470.0242-0.2967-0.2993-0.19630.169-0.051-0.39810.47060.01670.17420.27560.1878-0.2357-10.5619-19.304560.3148
190.1103-0.0073-0.0476-0.00030.01320.059-0.08730.0017-0.1359-0.6384-0.1243-0.90140.1613-0.243-0.00370.81310.01750.20521.2597-0.1691.253318.6622-30.897375.2235
200.38550.07850.23190.0568-0.07480.4643-0.14220.1788-0.4129-0.12560.0406-0.02280.19710.46370.05930.45340.04550.25270.4151-0.02480.6518-1.9216-51.688567.2419
210.07570.1176-0.04910.2743-0.14740.08920.0474-0.1827-0.5330.2183-0.0967-0.09150.6178-0.499-0.00441.27590.09620.2090.8218-0.08231.1448-17.2913-58.997769.7545
220.6582-0.0062-0.0030.8522-0.57370.38460.1026-0.401-0.18660.52340.0736-0.2939-0.2353-0.08810.25671.520.4938-0.0744-0.00340.18260.7855-6.7361-58.762986.5012
230.0776-0.0487-0.09680.08110.02470.1485-0.1084-0.00730.0061-0.0214-0.05710.0310.078-0.0765-0.04861.31040.3908-0.33960.5678-0.1080.4447-3.4692-49.511978.0923
240.3238-0.1674-0.0420.6652-0.09750.1663-0.0289-0.10490.00990.141-0.0628-0.03090.1020.0311-0.30110.77870.5668-0.11840.2670.40931.0625-7.8314-63.634584.2824
250.5847-0.1916-0.02650.34440.12810.4428-0.0363-0.23750.06830.55610.2239-0.60550.27830.24270.31730.46920.1280.03350.2263-0.37910.5235-10.1773-52.176253.9812
260.0485-0.08970.04560.22980.07890.59810.18150.0468-0.1278-0.1224-0.04450.12950.6995-0.6096-0.00370.58860.0916-0.04950.31930.0390.4421-26.2017-48.123446.8507
270.14860.1057-0.13660.0752-0.09710.1234-0.0389-0.0825-0.11010.0513-0.0335-0.02670.0340.0375-0.02111.7312-0.25320.20941.0771-0.01461.3378-50.1071-54.205940.063
280.37560.09030.1230.35940.00880.6654-0.0836-0.04-0.40410.00750.36680.12580.2889-0.37760.30050.47180.19870.0147-0.26080.20470.1622-29.9429-47.313845.0507
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESSEQ 13:42)
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESSEQ 43:160)
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESSEQ 161:272)
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESSEQ 273:316)
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESSEQ 317:350)
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESSEQ 92:119)
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESSEQ 120:151)
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESSEQ 152:198)
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESSEQ 199:211)
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESSEQ 212:225)
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESSEQ 226:251)
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESSEQ 252:302)
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESSEQ 303:310)
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESSEQ 311:358)
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESSEQ 13:42)
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESSEQ 43:160)
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESSEQ 161:272)
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESSEQ 273:316)
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESSEQ 317:350)
20X-RAY DIFFRACTION20CHAIN 'D' AND (RESSEQ 92:119)
21X-RAY DIFFRACTION21CHAIN 'D' AND (RESSEQ 120:151)
22X-RAY DIFFRACTION22CHAIN 'D' AND (RESSEQ 152:198)
23X-RAY DIFFRACTION23CHAIN 'D' AND (RESSEQ 199:211)
24X-RAY DIFFRACTION24CHAIN 'D' AND (RESSEQ 212:225)
25X-RAY DIFFRACTION25CHAIN 'D' AND (RESSEQ 226:251)
26X-RAY DIFFRACTION26CHAIN 'D' AND (RESSEQ 252:302)
27X-RAY DIFFRACTION27CHAIN 'D' AND (RESSEQ 303:310)
28X-RAY DIFFRACTION28CHAIN 'D' AND (RESSEQ 311:357)

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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