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- PDB-2ezw: Solution structure of the docking and dimerization domain of the ... -

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Basic information

Entry
Database: PDB / ID: 2ezw
TitleSolution structure of the docking and dimerization domain of the type I alpha regulatory subunit of protein kinase A (RIalpha D/D)
ComponentscAMP-dependent protein kinase type I-alpha regulatory subunitCAMP-dependent pathway
KeywordsTRANSFERASE / REGULATORY SUBUNIT / ANCHORING / FOUR-HELIX BUNDLE
Function / homology
Function and homology information


sperm connecting piece / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / PKA activation / Hedgehog 'off' state / nucleotide-activated protein kinase complex / cAMP-dependent protein kinase inhibitor activity ...sperm connecting piece / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / PKA activation / Hedgehog 'off' state / nucleotide-activated protein kinase complex / cAMP-dependent protein kinase inhibitor activity / sarcomere organization / cardiac muscle cell proliferation / cAMP-dependent protein kinase complex / Vasopressin regulates renal water homeostasis via Aquaporins / cellular response to glucagon stimulus / axoneme / negative regulation of activated T cell proliferation / protein kinase A catalytic subunit binding / plasma membrane raft / immunological synapse / mesoderm formation / cAMP binding / multivesicular body / regulation of protein phosphorylation / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / protein domain specific binding / negative regulation of gene expression / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / cAMP-dependent Protein Kinase, Chain A / cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain ...cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / cAMP-dependent Protein Kinase, Chain A / cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
cAMP-dependent protein kinase type I-alpha regulatory subunit
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodSOLUTION NMR / simulated annealing
AuthorsBanky, P.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Related Protein-Protein Interaction Modules Present Drastically Different Surface Topographies Despite A Conserved Helical Platform
Authors: Banky, P. / Roy, M. / Newlon, M.G. / Morikis, D. / Haste, N.M. / Taylor, S.S. / Jennings, P.A.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: Isoform-specific Differences between the Type Ia and IIa Cyclic-dependent Protein Kinase Anchoring Domains Revealed by Solution NMR
Authors: Banky, P. / Newlon, M.G. / Roy, M. / Garrod, S. / Taylor, S.S. / Jennings, P.A.
History
DepositionNov 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Derived calculations
Category: citation_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cAMP-dependent protein kinase type I-alpha regulatory subunit
B: cAMP-dependent protein kinase type I-alpha regulatory subunit


Theoretical massNumber of molelcules
Total (without water)12,0122
Polymers12,0122
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / -
RepresentativeModel #1

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Components

#1: Protein/peptide cAMP-dependent protein kinase type I-alpha regulatory subunit / CAMP-dependent pathway


Mass: 6005.980 Da / Num. of mol.: 2 / Fragment: dimerization-anchoring domain (residues 12-61)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: PRKAR1A (amino acids:12 - 61) / Plasmid: pRSETc / Production host: Escherichia coli (E. coli) / Strain (production host): EcoRI / References: UniProt: P00514, EC: 2.7.1.37

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D 1H-15N HSQC, amide proton exchange
1333D 1H-15N HSQC NOESY
1433D HNHA
1543D 13C-edited HMQC-NOESY
1653D 13C-edited(w2) 12C-filtered(w1) 13C-filtered(w3) NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
1R1a(12-61) at 1.2-1.6 mM dimer, 50mM sodium acetate, 150mM sodium chloride, pH 4.0, 90% H2O, 10% D2O90% H2O/10% D2O
215N-enriched R1a(12-61), 5% H2O, 95% D2O5% H2O, 95% D2O
315N-enriched R1a(12-61), 90% H2O, 10% D2O90% H2O/10% D2O
413C/15N-enriched R1a(12-61), 5% H2O, 95% D2O5% H2O, 95% D2O
5asymmetrically enriched 13C/15N-12C/14N R1a(12-61), 5% H2O,95% D2O5% H2O,95% D2O
Sample conditionsIonic strength: 50mM sodium acetate, 150mM sodium chloride / pH: 4. / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
FELIX95Molecular Simulations Inc.processing
X-PLOR3.851Brunger, A.T.structure solution
X-PLOR3.851Brunger, A.T.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 435 NOE-derived distance, 139 backbone dihedral and 13 hydrogen bond restraints per monomer
NMR ensembleConformers submitted total number: 18

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