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- PDB-1zxa: Solution Structure of the Coiled-Coil Domain of cGMP-dependent Pr... -

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Basic information

Entry
Database: PDB / ID: 1zxa
TitleSolution Structure of the Coiled-Coil Domain of cGMP-dependent Protein Kinase Ia
ComponentscGMP-dependent protein kinase 1, alpha isozyme
KeywordsTRANSFERASE / Parallel Coiled Coil Dimer
Function / homology
Function and homology information


negative regulation of glutamate secretion / negative regulation of inositol phosphate biosynthetic process / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / cell growth involved in cardiac muscle cell development / regulation of testosterone biosynthetic process / collateral sprouting / negative regulation of platelet aggregation / positive regulation of circadian rhythm / relaxation of vascular associated smooth muscle ...negative regulation of glutamate secretion / negative regulation of inositol phosphate biosynthetic process / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / cell growth involved in cardiac muscle cell development / regulation of testosterone biosynthetic process / collateral sprouting / negative regulation of platelet aggregation / positive regulation of circadian rhythm / relaxation of vascular associated smooth muscle / Rap1 signalling / regulation of GTPase activity / cGMP-mediated signaling / mitogen-activated protein kinase p38 binding / spermatid development / cGMP effects / negative regulation of vascular associated smooth muscle cell migration / negative regulation of vascular associated smooth muscle cell proliferation / dendrite development / cGMP binding / forebrain development / calcium channel regulator activity / cerebellum development / acrosomal vesicle / sarcolemma / neuron migration / actin cytoskeleton organization / positive regulation of cytosolic calcium ion concentration / Ca2+ pathway / protein kinase activity / protein phosphorylation / protein serine kinase activity / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
cGMP-dependent protein kinase, N-terminal coiled-coil domain / Coiled-coil N-terminus of cGMP-dependent protein kinase / cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / 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. ...cGMP-dependent protein kinase, N-terminal coiled-coil domain / Coiled-coil N-terminus of cGMP-dependent protein kinase / cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / 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 / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / 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
Similarity search - Domain/homology
cGMP-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, RDC refinement, analysis
AuthorsSchnell, J.R. / Zhou, G.P. / Zweckstetter, M. / Rigby, A.C. / Chou, J.J.
CitationJournal: Protein Sci. / Year: 2005
Title: Rapid and accurate structure determination of coiled-coil domains using NMR dipolar couplings: Application to cGMP-dependent protein kinase I{alpha}
Authors: Schnell, J.R. / Zhou, G.P. / Zweckstetter, M. / Rigby, A.C. / Chou, J.J.
History
DepositionJun 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: cGMP-dependent protein kinase 1, alpha isozyme
B: cGMP-dependent protein kinase 1, alpha isozyme


Theoretical massNumber of molelcules
Total (without water)15,2802
Polymers15,2802
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)20 / 20all calculated structures submitted
RepresentativeModel #20lowest energy

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Components

#1: Protein cGMP-dependent protein kinase 1, alpha isozyme / CGK 1 alpha / cGKI-alpha


Mass: 7639.798 Da / Num. of mol.: 2 / Fragment: N-terminal Coiled-Coil Domain, residues 1-58
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKG1, PRKGR1A / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q13976, 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
111TROSY version of HNCA, HN(CA)CB, HN(CA)CO
1212D 1H-15N spin echo Difference Experiments for 3-bond Jcc and Jnc measurement
131Standard HNCO-based 3D experiments for measuring one-bond J(NH), J(NC'), and J(C'Ca)
242Standard HNCO-based 3D experiments for measuring one-bond D(NH), D(NC'), and D(C'Ca)
151Standard 2D experiments for measuring 15N T1 and T2

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM cGK1a(1-59) U-15N,13C, 85%-2H, 20 mM phosphate buffer NA, 10 mM NaCl, 1 mM EDTA, 5 mM DTT, 1 mM azide, 95% H2O, 5% D2O95% H2O/5% D2O
21 mM cGK1a(1-59) U-15N,13C, 85%-2H, 20 mM phosphate buffer NA, 10 mM NaCl, 1 mM EDTA, 5 mM DTT, 1 mM azide, 15 mg/ml Pf1, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
130 mM salt 7ambient 303 K
230 mM salt 7ambient 303 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 AVANCEBrukerAVANCE5001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe2.2Delaglioprocessing
XPLOR-NIH2.9.9refinement
PALES1Zweckstetterstructure solution
RefinementMethod: simulated annealing, RDC refinement, analysis / Software ordinal: 1
Details: Structure determination consists of five steps. 1. Measure RDCs in Pf1 alignment medium. 2. Identify the coiled-coil motif by RDC-based molecular replacement analysis. 3) Define the subtle ...Details: Structure determination consists of five steps. 1. Measure RDCs in Pf1 alignment medium. 2. Identify the coiled-coil motif by RDC-based molecular replacement analysis. 3) Define the subtle curvature and super-coiling of the constituent helices by RDC refinement 4) Assemble parallel and anti-parallel models of the coiled-coil dimer using knowledge-based inter-molecular distance restraints. 5) Derive the correct monomer-monomer orientation by comparing experimental RDCs with those predicted from the 3D charge distribution and shape of the alternative structural models.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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