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- PDB-1r2a: THE MOLECULAR BASIS FOR PROTEIN KINASE A ANCHORING REVEALED BY SO... -

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Basic information

Entry
Database: PDB / ID: 1r2a
TitleTHE MOLECULAR BASIS FOR PROTEIN KINASE A ANCHORING REVEALED BY SOLUTION NMR
ComponentsPROTEIN (CAMP-DEPENDENT PROTEIN KINASE TYPE II REGULATORY SUBUNIT)
KeywordsTRANSFERASE / REGULATORY SUBUNIT / ANCHORING / FOUR-HELIX BUNDLE
Function / homology
Function and homology information


PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / DARPP-32 events / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / GPER1 signaling / Hedgehog 'off' state / Factors involved in megakaryocyte development and platelet production / cAMP-dependent protein kinase regulator activity / cAMP-dependent protein kinase inhibitor activity ...PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / DARPP-32 events / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / GPER1 signaling / Hedgehog 'off' state / Factors involved in megakaryocyte development and platelet production / cAMP-dependent protein kinase regulator activity / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase complex / protein kinase A catalytic subunit binding / small molecule binding / beta-2 adrenergic receptor binding / cAMP binding / T-tubule / regulation of protein phosphorylation / modulation of chemical synaptic transmission / protein domain specific binding / glutamatergic synapse / synapse / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex / identical protein binding / cytoplasm / cytosol
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 II-alpha regulatory subunit
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / DISTANCE GEOMETRY-SIMULATED ANNEALING
AuthorsNewlon, M.G. / Roy, M. / Morikis, D. / Hausken, Z.E. / Coghlan, V. / Scott, J.D. / Jennings, P.A.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: The molecular basis for protein kinase A anchoring revealed by solution NMR.
Authors: Newlon, M.G. / Roy, M. / Morikis, D. / Hausken, Z.E. / Coghlan, V. / Scott, J.D. / Jennings, P.A.
#1: Journal: Proteins / Year: 1993
Title: A Calculation Strategy for the Structure Determination of Symmetric Dimers by 1H NMR
Authors: Nilges, M.
History
DepositionDec 7, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 16, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (CAMP-DEPENDENT PROTEIN KINASE TYPE II REGULATORY SUBUNIT)
B: PROTEIN (CAMP-DEPENDENT PROTEIN KINASE TYPE II REGULATORY SUBUNIT)


Theoretical massNumber of molelcules
Total (without water)10,7962
Polymers10,7962
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)17 / 49LEAST RESTRAINT VIOLATION
RepresentativeModel #10

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Components

#1: Protein/peptide PROTEIN (CAMP-DEPENDENT PROTEIN KINASE TYPE II REGULATORY SUBUNIT) / RIIA(1-44)


Mass: 5398.181 Da / Num. of mol.: 2 / Fragment: DIMERIZATION-ANCHORING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: RIIA(1-44) / Plasmid: PET-16B / Production host: Escherichia coli (E. coli) / References: UniProt: P12367, 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
1113D NOESY-HSQC
1213D TOCSY-HMQC
131CBCA(CO)NH
141HNCA
151HN(CO)CA
16113C FILTERED NOESY
171HNHA
1812D NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED RIIALPHA(1-44). 13C FILTERED EXPERIMENTS ON A 50% 13C,15N LABELED, 50% UNLABELED RIIALPHA(1-44) SAMPLE ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED RIIALPHA(1-44). 13C FILTERED EXPERIMENTS ON A 50% 13C,15N LABELED, 50% UNLABELED RIIALPHA(1-44) SAMPLE WERE USED TO OBTAIN INTERMOLECULAR CONTACTS OF THE HOMODIMER.

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Sample preparation

Sample conditionsIonic strength: 0.012 mM / pH: 4.0 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX500 / Manufacturer: Bruker / Model: DMX500 / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
XPLORstructure solution
RefinementMethod: DISTANCE GEOMETRY-SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATIONS ABOVE
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 49 / Conformers submitted total number: 17

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