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- PDB-2drn: Docking and dimerization domain (D/D) of the Type II-alpha regula... -

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Basic information

Entry
Database: PDB / ID: 2drn
TitleDocking and dimerization domain (D/D) of the Type II-alpha regulatory subunity of protein kinase A (PKA) in complex with a peptide from an A-kinase anchoring protein
Components
  • 24-residues peptide from an a-kinase anchoring protein
  • cAMP-dependent protein kinase type II-alpha regulatory subunit
KeywordsTRANSFERASE / AKAP / PKA / signal transduction / 4-helix bundle / helix-loop-helix / protein-peptide complex
Function / homology
Function and homology information


regulation of sarcomere organization / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / DARPP-32 events / Factors involved in megakaryocyte development and platelet production / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / Hedgehog 'off' state / PKA activation / negative regulation of cAMP/PKA signal transduction ...regulation of sarcomere organization / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / DARPP-32 events / Factors involved in megakaryocyte development and platelet production / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / Hedgehog 'off' state / PKA activation / negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase regulator activity / nucleotide-activated protein kinase complex / MAP-kinase scaffold activity / cardiac muscle cell differentiation / regulation of Rho protein signal transduction / Vasopressin regulates renal water homeostasis via Aquaporins / regulation of small GTPase mediated signal transduction / cAMP-dependent protein kinase inhibitor activity / beta-2 adrenergic receptor binding / cAMP-dependent protein kinase complex / protein kinase A binding / NRAGE signals death through JNK / positive regulation of Rho protein signal transduction / RHOB GTPase cycle / small molecule binding / adrenergic receptor signaling pathway / RHOC GTPase cycle / plasma membrane raft / protein kinase A catalytic subunit binding / axoneme / RHOA GTPase cycle / cAMP binding / T-tubule / guanyl-nucleotide exchange factor activity / bone development / regulation of protein phosphorylation / modulation of chemical synaptic transmission / small GTPase binding / G alpha (12/13) signalling events / heart development / cell cortex / positive regulation of canonical NF-kappaB signal transduction / molecular adaptor activity / G protein-coupled receptor signaling pathway / protein domain specific binding / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / synapse / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex / identical protein binding / membrane / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
RII binding domain / RII 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 / : ...RII binding domain / RII 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 / : / ARHGEF1-like, PH domain / PH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / C1-like domain superfamily / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / RmlC-like jelly roll fold / PH-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
cAMP-dependent protein kinase type II-alpha regulatory subunit / A-kinase anchor protein 13 / A-kinase anchor protein 13
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
AuthorsNewlon, M.G. / Roy, M. / Morikis, D. / Hausken, Z.E. / Coghlan, V. / Scott, J.D. / Jennings, P.A.
CitationJournal: Embo J. / Year: 2001
Title: A novel mechanism of PKA anchoring revealed by solution structures of anchoring complexes.
Authors: Newlon, M.G. / Roy, M. / Morikis, D. / Carr, D.W. / Westphal, R. / Scott, J.D. / Jennings, P.A.
History
DepositionJun 11, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 29, 2024Group: 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: cAMP-dependent protein kinase type II-alpha regulatory subunit
B: cAMP-dependent protein kinase type II-alpha regulatory subunit
C: 24-residues peptide from an a-kinase anchoring protein


Theoretical massNumber of molelcules
Total (without water)13,3303
Polymers13,3303
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)13 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide cAMP-dependent protein kinase type II-alpha regulatory subunit


Mass: 5398.181 Da / Num. of mol.: 2
Fragment: N-terminal docking and dimerization domain, residues 4-46
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: RIIA(1-44) / Plasmid: PET-16B / Production host: Escherichia coli (E. coli) / References: UniProt: P12368, EC: 2.7.1.37
#2: Protein/peptide 24-residues peptide from an a-kinase anchoring protein / Fragment / Human thyroid anchoring protein / Ht31(493-515) peptide


Mass: 2533.828 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide has been generated by solid phase peptide synthesis.; This sequence occurs naturally in humans.
References: UniProt: Q14572, UniProt: Q12802*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: This structure was determined using standard 2d and 3d heteronuclear and homonuclear techniques.

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Sample preparation

DetailsContents: 2mM RII-alpha(1-44); 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851brungerstructure solution
X-PLOR3.851brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1370 restraints, 1247 are noe-derived distance restraints, 50 dihedral angle restraints,73 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 13

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