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- PDB-7e11: Crystal structure of PKAc-PLN R9C complex -

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Basic information

Entry
Database: PDB / ID: 700000000000
TitleCrystal structure of PKAc-PLN R9C complex
Components
  • PLN
  • cAMP-dependent protein kinase catalytic subunit alpha
KeywordsTRANSFERASE / Kinase / 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 / PKA activation / Regulation of insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / GPER1 signaling / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion ...PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Regulation of insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / 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 / 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 / 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 / Regulation of PLK1 Activity at G2/M Transition / CD209 (DC-SIGN) signaling / RET signaling / Mitochondrial protein degradation / VEGFA-VEGFR2 Pathway / Ion homeostasis / cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / regulation of osteoblast differentiation / cellular response to cold / sperm capacitation / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / protein kinase A regulatory subunit binding / intracellular potassium ion homeostasis / mesoderm formation / cAMP/PKA signal transduction / plasma membrane raft / axoneme / sperm flagellum / postsynaptic modulation of chemical synaptic transmission / negative regulation of TORC1 signaling / sperm midpiece / regulation of proteasomal protein catabolic process / positive regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / acrosomal vesicle / protein export from nucleus / positive regulation of phagocytosis / positive regulation of protein export from nucleus / negative regulation of smoothened signaling pathway / neural tube closure / neuromuscular junction / cellular response to glucose stimulus / positive regulation of cholesterol biosynthetic process / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / modulation of chemical synaptic transmission / peptidyl-serine phosphorylation / mRNA processing / adenylate cyclase-activating G protein-coupled receptor signaling pathway / manganese ion binding / cellular response to heat / protein kinase activity / postsynapse / regulation of cell cycle / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / ubiquitin protein ligase binding / centrosome / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / magnesium ion binding / negative regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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 ...cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.43 Å
AuthorsQin, J. / Lin, L. / Yuchi, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32022073 China
CitationJournal: Elife / Year: 2022
Title: Structures of PKA-phospholamban complexes reveal a mechanism of familial dilated cardiomyopathy.
Authors: Qin, J. / Zhang, J. / Lin, L. / Haji-Ghassemi, O. / Lin, Z. / Woycechowsky, K.J. / Van Petegem, F. / Zhang, Y. / Yuchi, Z.
History
DepositionJan 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: PLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4065
Polymers40,8522
Non-polymers5553
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-24 kcal/mol
Surface area15260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.910, 104.883, 168.096
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 39542.129 Da / Num. of mol.: 1
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 PLN


Mass: 1309.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestY
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: 2.75 Å3/Da / Density % sol: 55.31 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, pH 7.5 25% PEG 3350, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.43→50 Å / Num. obs: 6110 / % possible obs: 96.8 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.075 / Rrim(I) all: 0.182 / Χ2: 0.98 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.45-3.515.70.7382730.7760.3230.8080.85798.2
3.51-3.575.60.6293150.8980.2740.6880.53898.1
3.57-3.645.40.63200.8850.2660.6580.68499.1
3.64-3.725.40.4632940.9530.2080.5090.99599.3
3.72-3.85.70.4572940.90.2010.5010.73997.7
3.8-3.895.40.3623200.9370.160.3961.00999.1
3.89-3.985.60.3352930.9420.1490.3681.02998.3
3.98-4.095.60.2792980.950.1230.3060.85597.1
4.09-4.215.40.2283200.9720.1010.251.05897.9
4.21-4.355.70.1952920.9870.0870.2141.09398.6
4.35-4.55.40.1693060.9910.0750.1861.10596.2
4.5-4.685.50.1823060.9870.0820.21.15898.4
4.68-4.8950.1553120.9840.0720.1721.0196.9
4.89-5.155.20.1353000.9890.0630.151.16698.4
5.15-5.474.90.1473030.9810.070.1631.06995.9
5.47-5.94.50.1312940.9860.0640.1461.03689.4
5.9-6.4950.1353070.9890.0630.1491.02995.3
6.49-7.435.70.1053070.9960.0450.1151.10795.3
7.43-9.355.50.0933190.9850.0430.1031.06896.7
9.35-504.90.0943370.9940.0460.1051.07892.6

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Processing

Software
NameVersionClassification
PHENIX1.14_3247refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2cpk

2cpk


Resolution: 3.43→44.189 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3168 609 10.02 %
Rwork0.2565 5470 -
obs0.2624 6079 96.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.62 Å2 / Biso mean: 95.8112 Å2 / Biso min: 81.34 Å2
Refinement stepCycle: final / Resolution: 3.43→44.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2775 0 33 0 2808
Biso mean--86.85 --
Num. residues----349
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.43-3.77450.3811460.3187131596
3.7745-4.32030.32661530.2728137698
4.3203-5.44160.28091540.2515137697
5.4416-44.1890.3151560.2334140394

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