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- PDB-6mm8: Catalytic subunit of cAMP-dependent protein kinase A in complex w... -

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Basic information

Entry
Database: PDB / ID: 6mm8
TitleCatalytic subunit of cAMP-dependent protein kinase A in complex with RyR2 K2879A, S2813D phosphomimetic (2699-2904) crystal form 2
Components
  • Ryanodine receptor 2
  • cAMP-dependent protein kinase catalytic subunit alpha
KeywordsPROTEIN BINDING / Kinase / complex / ion channel / enzyme
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
ACETIC ACID / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DI(HYDROXYETHYL)ETHER / 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 30, 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
C: cAMP-dependent protein kinase catalytic subunit alpha
D: Ryanodine receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,96212
Polymers63,8842
Non-polymers1,07810
Water9,062503
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint4 kcal/mol
Surface area28260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.643, 67.860, 58.529
Angle α, β, γ (deg.)90.000, 92.220, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules CD

#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 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.: 1 / 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, 513 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ACY / ACETIC ACID


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


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.15 M HEPES pH 7.5, 15% (w/v) PEG 20k, and 25% (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2017
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: 58151 / % possible obs: 96.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.038 / Rrim(I) all: 0.074 / Χ2: 0.995 / Net I/σ(I): 6.5 / Num. measured all: 219079
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.92.90.57840890.7660.4090.7141.01181.7
1.9-1.973.50.48346750.8150.3030.5741.05894
1.97-2.043.90.3749470.8920.2170.4311.01499
2.04-2.123.90.27948990.9280.1650.3251.04298.6
2.12-2.213.80.20748880.9540.1240.2431.02998.2
2.21-2.333.70.14948910.9740.090.1751.00397.5
2.33-2.4840.12549300.9820.0730.1461.01499
2.48-2.673.90.149260.9850.0590.1161.01198
2.67-2.943.80.07449190.9910.0440.0870.97798
2.94-3.363.90.05649590.9940.0330.0650.95998.9
3.36-4.233.90.04249940.9950.0250.0490.92798.5
4.23-353.80.03950340.9950.0230.0460.91798.2

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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: 6MM7

6mm7


Resolution: 1.85→33.95 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.189 / SU ML: 0.092 / SU R Cruickshank DPI: 0.1365 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.132
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2214 2798 5 %RANDOM
Rwork0.1808 ---
obs0.1828 52992 92.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 104.48 Å2 / Biso mean: 26.447 Å2 / Biso min: 9.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20.23 Å2
2---0.02 Å20 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 1.85→33.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4372 0 98 503 4973
Biso mean--47.18 33.73 -
Num. residues----532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134642
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174304
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.6546279
X-RAY DIFFRACTIONr_angle_other_deg1.4021.58110005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36622.398246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93615838
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0171527
X-RAY DIFFRACTIONr_chiral_restr0.0730.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025072
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02995
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 99 -
Rwork0.304 1957 -
all-2056 -
obs--46.71 %

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