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- PDB-6mm5: Catalytic subunit of cAMP-dependent protein kinase A in complex w... -

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Basic information

Entry
Database: PDB / ID: 6mm5
TitleCatalytic subunit of cAMP-dependent protein kinase A in complex with RyR2 peptide (2799-2810)
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 / establishment of protein localization to endoplasmic reticulum / Rap1 signalling / 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 / establishment of protein localization to endoplasmic reticulum / Rap1 signalling / 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 / left ventricular cardiac muscle tissue morphogenesis / Vasopressin regulates renal water homeostasis via Aquaporins / suramin binding / GPER1 signaling / regulation of AV node cell action potential / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / 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 / MAPK6/MAPK4 signaling / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / GLI3 is processed to GLI3R by the proteasome / regulation of SA node cell action potential / AURKA Activation by TPX2 / Factors involved in megakaryocyte development and platelet production / Interleukin-3, Interleukin-5 and GM-CSF signaling / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / CD209 (DC-SIGN) signaling / RET signaling / Regulation of PLK1 Activity at G2/M Transition / Stimuli-sensing channels / regulation of ventricular cardiac muscle cell action potential / ventricular cardiac muscle cell action potential / positive regulation of sequestering of calcium ion / Mitochondrial protein degradation / VEGFA-VEGFR2 Pathway / embryonic heart tube morphogenesis / cardiac muscle hypertrophy / Ion homeostasis / calcium ion transport into cytosol / ryanodine-sensitive calcium-release channel activity / cAMP-dependent protein kinase / regulation of protein processing / response to caffeine / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to redox state / cAMP-dependent protein kinase activity / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cAMP-dependent protein kinase complex / cellular response to parathyroid hormone stimulus / cellular response to caffeine / calcium ion transmembrane import into cytosol / regulation of osteoblast differentiation / cellular response to cold / sperm capacitation / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / response to muscle activity / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / positive regulation of the force of heart contraction / intracellularly gated calcium channel activity / smooth endoplasmic reticulum / intracellular potassium ion homeostasis / mesoderm formation / cAMP/PKA signal transduction / plasma membrane raft / axoneme / detection of calcium ion / sperm flagellum / postsynaptic modulation of chemical synaptic transmission / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / positive regulation of heart rate / regulation of proteasomal protein catabolic process / negative regulation of TORC1 signaling / sperm midpiece / response to muscle stretch / calcium channel complex / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / positive regulation of gluconeogenesis / cellular response to epinephrine stimulus / acrosomal vesicle / sarcoplasmic reticulum membrane / regulation of heart rate / protein export from nucleus / positive regulation of phagocytosis / sarcoplasmic reticulum / positive regulation of protein export from nucleus / sarcomere / negative regulation of smoothened signaling pathway / neural tube closure / neuromuscular junction / cellular response to glucose stimulus / establishment of localization in cell / calcium-mediated signaling
Similarity search - Function
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 / cAMP-dependent protein kinase catalytic subunit / Ryanodine receptor Ryr ...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 / cAMP-dependent protein kinase catalytic subunit / Ryanodine receptor Ryr / RyR domain / 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. / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / 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: 1.95 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: cAMP-dependent protein kinase catalytic subunit alpha
C: Ryanodine receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6885
Polymers41,0962
Non-polymers5933
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-3 kcal/mol
Surface area15910 Å2
Unit cell
Length a, b, c (Å)54.861, 74.881, 98.561
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules EC

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


Mass: 39598.191 Da / Num. of mol.: 1 / Fragment: residues 16-351
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/peptide 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: 1497.681 Da / Num. of mol.: 1 / Fragment: residues 2799-2810 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: E9Q401

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Non-polymers , 4 types, 217 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M trimethylamine N-oxide, 0.1 M tris-HCl, 20% (w/v) PEG monomethyl ether 2K 25% (v/V) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.95→35 Å / Num. obs: 30237 / % possible obs: 99.5 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.027 / Rrim(I) all: 0.063 / Χ2: 0.92 / Net I/σ(I): 6.4 / Num. measured all: 157735
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-2.014.60.66124080.7750.3250.740.8997.5
2.01-2.074.90.52624860.8710.2540.5860.90899.6
2.07-2.155.10.37125040.9440.1770.4130.90199.8
2.15-2.235.10.28624650.9580.1370.3180.90599.7
2.23-2.335.60.21325210.9770.0970.2340.914100
2.33-2.465.50.16924970.9840.0770.1860.89999.9
2.46-2.615.20.13425060.9870.0630.1480.87499.8
2.61-2.815.30.09925160.9930.0460.1090.87199.8
2.81-3.095.50.06925270.9970.0320.0760.86299.6
3.09-3.545.20.04925320.9980.0230.0540.88299.6
3.54-4.465.60.03925780.9980.0180.0430.9799.7
4.46-3550.03626970.9980.0180.041.15499.1

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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: 3O7L

3o7l


Resolution: 1.95→32.95 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.575 / SU ML: 0.126 / SU R Cruickshank DPI: 0.1583 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.149
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 1484 4.9 %RANDOM
Rwork0.1804 ---
obs0.1826 28701 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 106.24 Å2 / Biso mean: 42.882 Å2 / Biso min: 26.31 Å2
Baniso -1Baniso -2Baniso -3
1-3.15 Å2-0 Å20 Å2
2---2.48 Å2-0 Å2
3----0.66 Å2
Refinement stepCycle: final / Resolution: 1.95→32.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2872 0 36 214 3122
Biso mean--35.82 49.51 -
Num. residues----350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133008
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172763
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.6524073
X-RAY DIFFRACTIONr_angle_other_deg1.4151.5816407
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4995354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81522.349166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.41315525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1531518
X-RAY DIFFRACTIONr_chiral_restr0.0670.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023320
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02673
LS refinement shellResolution: 1.949→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 85 -
Rwork0.31 2053 -
all-2138 -
obs--97.01 %

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