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- PDB-3o7l: Crystal Structure of phospholamban (1-19):PKA C-subunit:AMP-PNP:M... -

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Basic information

Entry
Database: PDB / ID: 3o7l
TitleCrystal Structure of phospholamban (1-19):PKA C-subunit:AMP-PNP:Mg2+ complex
Components
  • (cAMP-dependent protein kinase catalytic subunit ...CAMP-dependent pathway) x 2
  • Cardiac phospholamban
KeywordsTRANSFERASE / Protein Kinase A / Phospholamban / Allostery / Substrate Recognition / Conformational Selection / Intrinsically Disordered Proteins / Membrane Proteins
Function / homology
Function and homology information


negative regulation of calcium ion binding / negative regulation of calcium ion import into sarcoplasmic reticulum / negative regulation of ATPase-coupled calcium transmembrane transporter activity / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / regulation of relaxation of muscle / Ion transport by P-type ATPases / regulation of the force of heart contraction by cardiac conduction / calcium ion-transporting ATPase complex / spontaneous exocytosis of neurotransmitter / HDL assembly ...negative regulation of calcium ion binding / negative regulation of calcium ion import into sarcoplasmic reticulum / negative regulation of ATPase-coupled calcium transmembrane transporter activity / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / regulation of relaxation of muscle / Ion transport by P-type ATPases / regulation of the force of heart contraction by cardiac conduction / calcium ion-transporting ATPase complex / spontaneous exocytosis of neurotransmitter / HDL assembly / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion / GPER1 signaling / Hedgehog 'off' state / 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 / regulation of calcium ion import / 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 / negative regulation of heart contraction / Factors involved in megakaryocyte development and platelet production / CD209 (DC-SIGN) signaling / Regulation of PLK1 Activity at G2/M Transition / Interleukin-3, Interleukin-5 and GM-CSF signaling / ATPase inhibitor activity / RET signaling / regulation of the force of heart contraction / negative regulation of ATP-dependent activity / Ion homeostasis / regulation of cardiac muscle cell contraction / VEGFA-VEGFR2 Pathway / cardiac muscle tissue development / nucleotide-activated protein kinase complex / regulation of cellular respiration / regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / regulation of heart contraction / cAMP-dependent protein kinase / cellular response to cold / sperm capacitation / regulation of osteoblast differentiation / negative regulation of heart rate / cAMP-dependent protein kinase activity / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / postsynaptic modulation of chemical synaptic transmission / response to zinc ion / response to testosterone / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / axoneme / plasma membrane raft / calcium channel regulator activity / regulation of calcium ion transport / mesoderm formation / sperm flagellum / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / protein kinase A signaling / positive regulation of gluconeogenesis / regulation of ryanodine-sensitive calcium-release channel activity / Notch signaling pathway / regulation of synaptic transmission, glutamatergic / negative regulation of TORC1 signaling / sperm midpiece / sarcoplasmic reticulum membrane / protein export from nucleus / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / positive regulation of protein export from nucleus / sarcoplasmic reticulum / neural tube closure / cellular response to glucose stimulus / mitochondrial membrane / modulation of chemical synaptic transmission / neuromuscular junction / response to insulin / adenylate cyclase-activating G protein-coupled receptor signaling pathway / intracellular calcium ion homeostasis / positive regulation of insulin secretion / mRNA processing / small GTPase binding / calcium ion transport
Similarity search - Function
Phospholamban / Phospholamban / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...Phospholamban / Phospholamban / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 / DI(HYDROXYETHYL)ETHER / cAMP-dependent protein kinase catalytic subunit alpha / Cardiac phospholamban
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCheng, C.Y. / Taylor, S.S.
CitationJournal: Nat.Chem.Biol. / Year: 2010
Title: Dynamics connect substrate recognition to catalysis in protein kinase A.
Authors: Masterson, L.R. / Cheng, C. / Yu, T. / Tonelli, M. / Kornev, A. / Taylor, S.S. / Veglia, G.
History
DepositionJul 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: cAMP-dependent protein kinase catalytic subunit alpha
D: cAMP-dependent protein kinase catalytic subunit alpha
I: Cardiac phospholamban
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6347
Polymers82,9733
Non-polymers6614
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-35 kcal/mol
Surface area28760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.193, 92.193, 192.186
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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CAMP-dependent protein kinase catalytic subunit ... , 2 types, 2 molecules BD

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


Mass: 40577.340 Da / Num. of mol.: 1 / Fragment: phospholamban peptide
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pkaca, Prkaca / Production host: Escherichia coli (E. coli) / References: UniProt: P05132, cAMP-dependent protein kinase
#2: Protein cAMP-dependent protein kinase catalytic subunit alpha / CAMP-dependent pathway / PKA C-alpha


Mass: 40657.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pkaca, Prkaca / Production host: Escherichia coli (E. coli) / References: UniProt: P05132, cAMP-dependent protein kinase

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Protein/peptide , 1 types, 1 molecules I

#3: Protein/peptide Cardiac phospholamban / PLB


Mass: 1738.022 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemically synthesized. This sequence occurs naturally from Phospholamban
References: UniProt: P61014

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Non-polymers , 4 types, 25 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: 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
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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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: 2.84 Å3/Da / Density % sol: 56.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: The complex was obtained by combining a 1:10:10:10 molar ratio mixture of PKA-C (7 mg/ml), PLN1-19, MgCl2, and AMP-PNP in 20 mM sodium acetate (pH 6.5), 180 mM KCl, and 5 mM DTT, VAPOR ...Details: The complex was obtained by combining a 1:10:10:10 molar ratio mixture of PKA-C (7 mg/ml), PLN1-19, MgCl2, and AMP-PNP in 20 mM sodium acetate (pH 6.5), 180 mM KCl, and 5 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 26095 / % possible obs: 99.5 % / Observed criterion σ(F): 264629 / Observed criterion σ(I): 264629 / Redundancy: 10.5 % / Biso Wilson estimate: 51.6 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.063 / Net I/σ(I): 38.8
Reflection shellResolution: 2.8→2.88 Å / Mean I/σ(I) obs: 5.1 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ATP

1atp


Resolution: 2.8→39.086 Å / SU ML: 0.45 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1327 5.09 %RANDOM
Rwork0.216 ---
obs0.216 25304 99.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.117 Å2 / ksol: 0.288 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.6609 Å20 Å20 Å2
2--7.6609 Å2-0 Å2
3----15.3218 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5174 0 36 21 5231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065297
X-RAY DIFFRACTIONf_angle_d0.9517204
X-RAY DIFFRACTIONf_dihedral_angle_d19.3311782
X-RAY DIFFRACTIONf_chiral_restr0.068802
X-RAY DIFFRACTIONf_plane_restr0.004923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.90320.35891370.23692767X-RAY DIFFRACTION100
2.9032-3.05620.34041610.25012727X-RAY DIFFRACTION100
3.0562-3.24760.32921480.24682758X-RAY DIFFRACTION100
3.2476-3.49820.36081510.26012737X-RAY DIFFRACTION99
3.4982-3.850.32881520.24522681X-RAY DIFFRACTION97
3.85-4.40640.25961540.18952731X-RAY DIFFRACTION99
4.4064-5.54910.24851420.18672788X-RAY DIFFRACTION100
5.5491-39.09060.2481490.22192786X-RAY DIFFRACTION100
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)
11.6884-0.5333-0.65811.0574-0.80.9496-0.12260.2745-0.5068-0.4984-0.16520.54590.1614-0.4599-2.0574-0.2216-0.008-0.00670.00880.2412-0.1157-10.470232.06997.6142
20.73690.0179-0.24190.59790.05770.6067-0.012-0.34470.0730.27080.2006-0.0991-0.06290.23080.0203-0.0075-0.0083-0.09490.0553-0.1350.032517.734337.350733.9139
30.07190.0008-0.00970.0063-0.00430.0130.019-0.012-0.03140.03950.05610.02930.00990.01920.0619-0.005-0.03050.12050.03280.1420.1876.746732.70410.3398
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain B
2X-RAY DIFFRACTION2chain D
3X-RAY DIFFRACTION3chain i

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