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- PDB-5kjz: Co-crystal structure of PKA RI alpha CNB-B mutant (G316R/A336T) w... -

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Basic information

Entry
Database: PDB / ID: 5kjz
TitleCo-crystal structure of PKA RI alpha CNB-B mutant (G316R/A336T) with cGMP
ComponentscAMP-dependent protein kinase type I-alpha regulatory subunitCAMP-dependent pathway
KeywordsSIGNALING PROTEIN / Cyclic nucleotide / cAMP-dependent protein kinase / nucleotide selectivity / cyclic nucleotide binding domain
Function / homology
Function and homology information


sperm connecting piece / cAMP-dependent protein kinase regulator activity / negative regulation of cAMP-dependent protein kinase activity / ALK mutants bind TKIs / nucleotide-activated protein kinase complex / cAMP-dependent protein kinase inhibitor activity / sarcomere organization / cardiac muscle cell proliferation / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation ...sperm connecting piece / cAMP-dependent protein kinase regulator activity / negative regulation of cAMP-dependent protein kinase activity / ALK mutants bind TKIs / nucleotide-activated protein kinase complex / cAMP-dependent protein kinase inhibitor activity / sarcomere organization / cardiac muscle cell proliferation / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / ciliary base / cAMP-dependent protein kinase complex / cellular response to glucagon stimulus / negative regulation of activated T cell proliferation / protein kinase A catalytic subunit binding / plasma membrane raft / PKA activation in glucagon signalling / mesoderm formation / Signaling by ALK fusions and activated point mutants / DARPP-32 events / Hedgehog 'off' state / cAMP binding / multivesicular body / FCGR3A-mediated IL10 synthesis / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / intracellular signal transduction / protein domain specific binding / negative regulation of gene expression / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / protein-containing complex / membrane / cytosol / cytoplasm
Similarity search - Function
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. ...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 / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
CYCLIC GUANOSINE MONOPHOSPHATE / cAMP-dependent protein kinase type I-alpha regulatory subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.347 Å
AuthorsLorenz, R. / Moon, E. / Kim, J.J. / Huang, G.Y. / Kim, C. / Herberg, F.W.
Funding support Germany, United States, 3items
OrganizationGrant numberCountry
Federal Ministry of Education and Research GrantFKZ 0316177F (No Pain) Germany
the Center for Interdisciplinary Nanostructure Science and Technology (CINSaT) of University of Kassel Germany
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R01GM090161-06 United States
CitationJournal: Biochem. J. / Year: 2017
Title: Mutations of PKA cyclic nucleotide-binding domains reveal novel aspects of cyclic nucleotide selectivity.
Authors: Lorenz, R. / Moon, E.W. / Kim, J.J. / Schmidt, S.H. / Sankaran, B. / Pavlidis, I.V. / Kim, C. / Herberg, F.W.
History
DepositionJun 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Aug 2, 2017Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)17,6164
Polymers17,0871
Non-polymers5293
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.461, 67.780, 77.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsmonomer according to gel filtration

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Components

#1: Protein cAMP-dependent protein kinase type I-alpha regulatory subunit / CAMP-dependent pathway / Tissue-specific extinguisher 1 / TSE1


Mass: 17086.668 Da / Num. of mol.: 1 / Mutation: G316R, A336T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAR1A, PKR1, PRKAR1, TSE1 / Production host: Escherichia coli (E. coli) / Strain (production host): TP2000 delta cya / References: UniProt: P10644
#2: Chemical ChemComp-PCG / CYCLIC GUANOSINE MONOPHOSPHATE / Cyclic guanosine monophosphate


Mass: 345.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O7P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.04 M critic acid, 0.06 M Bis-Tris propane, 24% w/v PEG 1500, 20% v/v glycerol

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.347→25 Å / Num. obs: 34711 / % possible obs: 98.6 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 22.01
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 6.7 / % possible all: 83.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 1.347→24.264 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1818 1741 5.02 %
Rwork0.1523 --
obs0.1537 34711 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.347→24.264 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1187 0 35 236 1458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061274
X-RAY DIFFRACTIONf_angle_d1.0981728
X-RAY DIFFRACTIONf_dihedral_angle_d22.113505
X-RAY DIFFRACTIONf_chiral_restr0.085193
X-RAY DIFFRACTIONf_plane_restr0.005222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3474-1.38710.17911230.14152265X-RAY DIFFRACTION83
1.3871-1.43180.18911410.13252671X-RAY DIFFRACTION97
1.4318-1.4830.16711440.13232738X-RAY DIFFRACTION100
1.483-1.54240.1591470.12422777X-RAY DIFFRACTION100
1.5424-1.61250.15781440.12052748X-RAY DIFFRACTION100
1.6125-1.69750.14131460.12852775X-RAY DIFFRACTION100
1.6975-1.80390.19361460.14332768X-RAY DIFFRACTION100
1.8039-1.94310.181470.14672797X-RAY DIFFRACTION100
1.9431-2.13850.16451480.14432803X-RAY DIFFRACTION100
2.1385-2.44770.18921480.15282824X-RAY DIFFRACTION100
2.4477-3.08290.19481500.16882847X-RAY DIFFRACTION100
3.0829-24.26840.18531570.15782957X-RAY DIFFRACTION99

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