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- PDB-6mm7: Catalytic subunit of cAMP-dependent protein kinase A in complex w... -

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Basic information

Entry
Database: PDB / ID: 6mm7
TitleCatalytic subunit of cAMP-dependent protein kinase A in complex with RyR2 K2879A, S2813D phosphomimetic (2699-2904) crystal form 1
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


manganese ion transmembrane transport / spontaneous exocytosis of neurotransmitter / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / HDL assembly / positive regulation of triglyceride catabolic process / DARPP-32 events / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process ...manganese ion transmembrane transport / spontaneous exocytosis of neurotransmitter / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / HDL assembly / positive regulation of triglyceride catabolic process / DARPP-32 events / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Rap1 signalling / 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 / suramin binding / Vasopressin regulates renal water homeostasis via Aquaporins / regulation of AV node cell action potential / GPER1 signaling / 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 / sarcoplasmic reticulum calcium ion transport / Anchoring of the basal body to the plasma membrane / Recruitment of NuMA to mitotic centrosomes / regulation of SA node cell action potential / AURKA Activation by TPX2 / Factors involved in megakaryocyte development and platelet production / MAPK6/MAPK4 signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / CD209 (DC-SIGN) signaling / RET signaling / GLI3 is processed to GLI3R by the proteasome / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / calcium-induced calcium release activity / A band / Regulation of PLK1 Activity at G2/M Transition / Stimuli-sensing channels / regulation of ventricular cardiac muscle cell action potential / Mitochondrial protein degradation / VEGFA-VEGFR2 Pathway / : / ventricular cardiac muscle cell action potential / nucleotide-activated protein kinase complex / Ion homeostasis / cardiac muscle hypertrophy / embryonic heart tube morphogenesis / calcium ion transport into cytosol / regulation of cellular respiration / ryanodine-sensitive calcium-release channel activity / histone H1-4S35 kinase activity / cAMP-dependent protein kinase / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of protein processing / negative regulation of glycolytic process / response to redox state / cAMP-dependent protein kinase activity / regulation of cardiac muscle contraction by calcium ion signaling / cellular response to parathyroid hormone stimulus / protein localization to lipid droplet / cellular response to caffeine / regulation of bicellular tight junction assembly / cAMP-dependent protein kinase complex / extrinsic component of cytoplasmic side of plasma membrane / response to caffeine / interleukin-2-mediated signaling pathway / regulation of osteoblast differentiation / response to muscle activity / calcium ion transmembrane import into cytosol / sperm capacitation / cellular response to cold / negative regulation of cytosolic calcium ion concentration / ciliary base / protein kinase A regulatory subunit binding / negative regulation of glycolytic process through fructose-6-phosphate / 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 / TORC1 signaling / plasma membrane raft / response to magnesium ion / cAMP/PKA signal transduction / axoneme / detection of calcium ion / regulation of cardiac muscle contraction / sperm flagellum / postsynaptic modulation of chemical synaptic transmission / positive regulation of heart rate / regulation of cytosolic calcium ion concentration / regulation of synaptic transmission, glutamatergic / striated muscle contraction / response to muscle stretch / cardiac muscle contraction / release of sequestered calcium ion into cytosol
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
ACETIC ACID / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / FORMIC ACID / 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: 1.85 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 1.3Oct 23, 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
A: cAMP-dependent protein kinase catalytic subunit alpha
C: Ryanodine receptor 2
D: cAMP-dependent protein kinase catalytic subunit alpha
E: Ryanodine receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,71424
Polymers127,7684
Non-polymers1,94620
Water14,952830
1
A: cAMP-dependent protein kinase catalytic subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4118
Polymers39,5981
Non-polymers8127
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Ryanodine receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3482
Polymers24,2861
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: cAMP-dependent protein kinase catalytic subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,57211
Polymers39,5981
Non-polymers97410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
E: Ryanodine receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3833
Polymers24,2861
Non-polymers982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.337, 67.560, 176.852
Angle α, β, γ (deg.)90.000, 90.730, 90.000
Int Tables number3
Space group name H-MP121

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Components

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Protein , 2 types, 4 molecules ADCE

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


Mass: 39598.191 Da / Num. of mol.: 2 / 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 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: 24285.613 Da / Num. of mol.: 2 / Fragment: residues 2699-2904 / Mutation: K2879A, S2813D
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, 850 molecules

#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: 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
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 830 / 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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M magnesium formate and 25% (w/v) PEG 3350; 0.05 M HEPES, and 25% 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: 1.85→35 Å / Num. obs: 111231 / % possible obs: 94.4 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.027 / Rrim(I) all: 0.071 / Χ2: 1.059 / Net I/σ(I): 11.3 / Num. measured all: 698657
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.896.40.79372140.90.3260.8591.13491.8
1.89-1.944.10.50468280.9370.2660.5732.22187.2
1.94-1.996.30.47372380.950.1960.5130.81992.9
1.99-2.056.30.35272610.9520.1460.3821.05193.2
2.05-2.126.20.2773270.9720.1130.2931.08793.8
2.12-2.196.20.21973880.9780.0930.2381.05894.6
2.19-2.284.40.1654430.9770.0890.1841.30769.6
2.28-2.386.20.13575760.990.0580.1480.80697
2.38-2.516.20.1177290.9930.0470.121.00798.4
2.51-2.676.40.09578140.9950.040.1041.06599.4
2.67-2.876.60.08678400.9950.0360.0941.03599.9
2.87-3.166.90.07178610.9970.0290.0771.001100
3.16-3.627.10.05678570.9980.0220.060.93499.6
3.62-4.566.80.04877730.9980.0190.0521.03698.1
4.56-357.30.04380820.9980.0170.0471.04799.8

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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: 6MM6

6mm6


Resolution: 1.85→33.8 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.157 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.139
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 5806 5.2 %RANDOM
Rwork0.212 ---
obs0.2134 105173 94.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 128.62 Å2 / Biso mean: 37.297 Å2 / Biso min: 19.16 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å2-0 Å20.04 Å2
2--1.93 Å20 Å2
3----0.18 Å2
Refinement stepCycle: final / Resolution: 1.85→33.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8654 0 120 830 9604
Biso mean--45.48 40.54 -
Num. residues----1063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0139042
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178323
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.65112217
X-RAY DIFFRACTIONr_angle_other_deg1.2941.58219297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16751075
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.14722.317479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.014151595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5371553
X-RAY DIFFRACTIONr_chiral_restr0.0690.21146
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029976
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021969
LS refinement shellResolution: 1.849→1.897 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 393 -
Rwork0.294 7514 -
all-7907 -
obs--90.55 %
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)
12.84320.11990.58140.01860.10450.79960.03170.1153-0.00720.0076-0.00730.0127-0.0455-0.1013-0.02440.06370.01460.03480.02790.00490.071-0.2919.10819.803
22.97550.91111.45351.35821.08671.2728-0.25650.39910.2475-0.49370.13290.1486-0.31970.04630.12360.3243-0.0492-0.03540.20790.04560.1129.75751.5629.698
33.409-0.01440.47580.1345-0.05030.47210.0144-0.1930.0798-0.0060.005-0.019-0.03660.0593-0.01940.0046-0.01020.00510.0309-0.01350.008-6.412-13.80168.071
41.8953-0.95310.80231.6267-0.75090.6113-0.0918-0.3217-0.02270.38830.116-0.0952-0.0373-0.0108-0.02420.27910.0443-0.00820.1386-0.03590.1067-3618.11858.455
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 350
2X-RAY DIFFRACTION1A401 - 405
3X-RAY DIFFRACTION2C2699 - 2904
4X-RAY DIFFRACTION3D15 - 350
5X-RAY DIFFRACTION3D401 - 404
6X-RAY DIFFRACTION4E2699 - 2904

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