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- PDB-6mm6: Catalytic subunit of cAMP-dependent protein kinase A in complex w... -

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Basic information

Entry
Database: PDB / ID: 6mm6
TitleCatalytic subunit of cAMP-dependent protein kinase A in complex with RyR2 phosphorylation domain (2699-2904)
Components
  • Ryanodine receptor 2
  • cAMP-dependent protein kinase catalytic subunit alpha
KeywordsTRANSFERASE/PROTEIN BINDING / Kinase / complex / ion channel / enzyme / PROTEIN BINDING / TRANSFERASE-PROTEIN BINDING complex
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 / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / regulation of atrial cardiac muscle cell action potential / PKA activation ...PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / HDL assembly / DARPP-32 events / Rap1 signalling / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / regulation of atrial cardiac muscle cell action potential / PKA activation / Regulation of insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / left ventricular cardiac muscle tissue morphogenesis / GPER1 signaling / suramin binding / Hedgehog 'off' state / regulation of AV node cell action potential / 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 / regulation of SA node cell action potential / 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 / Stimuli-sensing channels / regulation of ventricular cardiac muscle cell action potential / ventricular cardiac muscle cell action potential / Mitochondrial protein degradation / Ion homeostasis / positive regulation of sequestering of calcium ion / VEGFA-VEGFR2 Pathway / embryonic heart tube morphogenesis / cardiac muscle hypertrophy / calcium ion transport into cytosol / ryanodine-sensitive calcium-release channel activity / response to caffeine / cAMP-dependent protein kinase / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of protein processing / response to redox state / cAMP-dependent protein kinase activity / calcium ion transmembrane import into cytosol / 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 / response to muscle activity / sperm capacitation / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / cellular response to caffeine / positive regulation of the force of heart contraction / intracellularly gated calcium channel activity / mesoderm formation / cAMP/PKA signal transduction / sperm flagellum / plasma membrane raft / axoneme / detection of calcium ion / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / postsynaptic modulation of chemical synaptic transmission / smooth endoplasmic reticulum / positive regulation of heart rate / negative regulation of TORC1 signaling / response to muscle stretch / regulation of proteasomal protein catabolic process / sarcoplasmic reticulum membrane / cellular response to epinephrine stimulus / sperm midpiece / calcium channel complex / positive regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / regulation of heart rate / protein export from nucleus / acrosomal vesicle / sarcoplasmic reticulum / sarcomere / positive regulation of protein export from nucleus / negative regulation of smoothened signaling pathway / establishment of localization in cell / neural tube closure / positive regulation of cholesterol biosynthetic process / modulation of chemical synaptic transmission / calcium-mediated signaling / cellular response to glucose stimulus
Similarity search - Function
Globin-like - #160 / Ryanodine receptor, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr ...Globin-like - #160 / Ryanodine receptor, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain / cAMP-dependent protein kinase catalytic subunit / RyR/IP3 receptor binding core, RIH domain superfamily / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / RyR and IP3R Homology associated / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / : / MIR motif / MIR domain / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Mir domain superfamily / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Globin-like / EF-hand domain pair / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
ACETATE ION / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / TRIETHYLENE GLYCOL / Ryanodine receptor 2 / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
Authorsvan Petegem, F. / Haji-Ghassemi, O.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT 153305 Canada
CitationJournal: Mol.Cell / Year: 2019
Title: cAMP-dependent protein kinase A in complex with RyR2 peptide (2799-2810)
Authors: Haji-Ghassemi, O. / Yuchi, Z. / van Petegem, F.
History
DepositionSep 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: 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 1.3Nov 6, 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
C: cAMP-dependent protein kinase catalytic subunit alpha
E: cAMP-dependent protein kinase catalytic subunit alpha
F: Ryanodine receptor 2
D: Ryanodine receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,10212
Polymers127,7124
Non-polymers1,3908
Water6,575365
1
C: cAMP-dependent protein kinase catalytic subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3495
Polymers39,5981
Non-polymers7514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
E: cAMP-dependent protein kinase catalytic subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2024
Polymers39,5981
Non-polymers6043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
F: Ryanodine receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2932
Polymers24,2581
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ryanodine receptor 2


Theoretical massNumber of molelcules
Total (without water)24,2581
Polymers24,2581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.451, 74.944, 88.690
Angle α, β, γ (deg.)105.510, 90.140, 94.390
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 4 molecules CEFD

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


Mass: 39598.191 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 (E. coli) / References: UniProt: P05132, cAMP-dependent protein kinase
#2: Protein Ryanodine receptor 2 / RyR2 / Cardiac muscle ryanodine receptor / Cardiac muscle ryanodine receptor-calcium release ...RyR2 / Cardiac muscle ryanodine receptor / Cardiac muscle ryanodine receptor-calcium release channel / Type 2 ryanodine receptor


Mass: 24257.604 Da / Num. of mol.: 2 / Fragment: residues 2699-2904 / Mutation: K2879A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ryr2 / Production host: Escherichia coli (E. coli) / References: UniProt: E9Q401

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Non-polymers , 6 types, 373 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.05M HEPES, 0.05 M KCl, 0.01M MgCl2, 15% (w/v) PEG 6K, and 25% (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.39→35 Å / Num. obs: 56090 / % possible obs: 98.5 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.108 / Rrim(I) all: 0.161 / Χ2: 1.011 / Net I/σ(I): 5.2 / Num. measured all: 123858
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.2 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.39-2.460.73546550.4580.670.9980.90897.8
2.46-2.540.66746390.490.6090.9060.89797.9
2.54-2.630.53546330.6130.4870.7250.93298.2
2.63-2.740.44246550.7190.4030.60.95998.2
2.74-2.860.32846850.8190.2990.4460.96498.3
2.86-3.010.24346760.880.2220.331.01698.5
3.01-3.20.17646900.9380.1610.2391.10998.7
3.2-3.450.12546850.9670.1140.1691.18498.6
3.45-3.790.08446910.9820.0770.1141.18598.8
3.79-4.340.0646850.990.0550.0821.02298.9
4.34-5.470.04947040.9920.0450.0671.05799
5.47-350.03846920.9960.0340.0510.89798.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MM5

6mm5


Resolution: 2.39→34.87 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.892 / SU B: 22.792 / SU ML: 0.253 / SU R Cruickshank DPI: 0.3972 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.397 / ESU R Free: 0.264
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 2830 5 %RANDOM
Rwork0.2235 ---
obs0.2254 53257 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 114.21 Å2 / Biso mean: 38.839 Å2 / Biso min: 15.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å2-0.59 Å2-0.85 Å2
2--0.15 Å20.23 Å2
3----0.64 Å2
Refinement stepCycle: final / Resolution: 2.39→34.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8512 0 145 365 9022
Biso mean--57.95 34.5 -
Num. residues----1041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138876
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178174
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.65312014
X-RAY DIFFRACTIONr_angle_other_deg1.2091.58118962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4351035
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97822.263464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.515151570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3161552
X-RAY DIFFRACTIONr_chiral_restr0.0640.21134
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029680
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021910
LS refinement shellResolution: 2.393→2.455 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 199 -
Rwork0.324 3850 -
all-4049 -
obs--96.27 %
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)
13.0444-0.2014-0.53060.31920.01621.2074-0.01570.0523-0.0149-0.00760.02390.0596-0.0296-0.0807-0.00820.0409-0.00690.0820.2695-0.06820.199347.3893-33.2-196.6503
22.95760.1895-0.68370.65910.27821.28150.0048-0.08670.01620.00390.0244-0.11320.00340.0841-0.02930.03950.01910.07330.3407-0.07750.195339.2226-25.7699-155.6884
32.40250.592-0.47031.8191-0.99151.6937-0.11810.399-0.1159-0.62690.05130.05660.2289-0.10730.06680.3198-0.00220.11610.581-0.11920.276812.1012-57.2789-149.1702
43.0244-0.9403-1.011.30561.19262.1066-0.1027-0.2519-0.13380.49580.0965-0.07020.37270.18030.00620.32750.02180.11970.4465-0.07020.313880.7731-65.2663-203.4741
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C18 - 401
2X-RAY DIFFRACTION2E18 - 350
3X-RAY DIFFRACTION3F2701 - 2904
4X-RAY DIFFRACTION4D2700 - 2904

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