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- PDB-4jv4: Crystal Structure of RIalpha(91-379) bound to HE33, a N6 di-propy... -

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Basic information

Entry
Database: PDB / ID: 4jv4
TitleCrystal Structure of RIalpha(91-379) bound to HE33, a N6 di-propyl substituted cAMP analog
ComponentscAMP-dependent protein kinase type I-alpha regulatory subunitCAMP-dependent pathway
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / cAMP-dependent protein kinase / cyclic nucleotide analogs / isoform selectivity / fluorescence anisotropy / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / nucleotide-activated protein kinase complex / Hedgehog 'off' state / 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 / nucleotide-activated protein kinase complex / Hedgehog 'off' state / cAMP-dependent protein kinase inhibitor activity / cardiac muscle cell proliferation / cAMP-dependent protein kinase complex / sarcomere organization / 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 / mesoderm formation / immunological synapse / cAMP binding / multivesicular body / regulation of protein phosphorylation / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / 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 / 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
Chem-1OR / cAMP-dependent protein kinase type I-alpha regulatory subunit
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.952 Å
AuthorsBrown, S.H.J. / Cheng, C.Y. / Saldanha, A.S. / Wu, J. / Cottam, H. / Sankaran, B. / Taylor, S.S.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Implementing Fluorescence Anisotropy Screening and Crystallographic Analysis to Define PKA Isoform-Selective Activation by cAMP Analogs.
Authors: Brown, S.H. / Cheng, C.Y. / Saldanha, S.A. / Wu, J. / Cottam, H.B. / Sankaran, B. / Taylor, S.S.
History
DepositionMar 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)33,3213
Polymers32,4941
Non-polymers8272
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.830, 89.830, 185.055
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 32493.854 Da / Num. of mol.: 1 / Fragment: RIalpha (93-380) / Mutation: deletion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: PRKAR1A / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / References: UniProt: P00514
#2: Chemical ChemComp-1OR / (2R,4aR,6R,7R,7aS)-6-[6-(dipropylamino)-9H-purin-9-yl]tetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinine-2,7-diol 2-oxide


Mass: 413.365 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H24N5O6P

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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: 3.32 Å3/Da / Density % sol: 62.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 6.3% PEG 3350, 0.074 M sodium malonate (pH 7.0) after 3 weeks of growth, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 30, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 9906 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Redundancy: 9.2 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 40.6
Reflection shellResolution: 2.95→3 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 3.3 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NE6

1ne6


Resolution: 2.952→44.915 Å / SU ML: 0.39 / Isotropic thermal model: ANISOTROPIC / σ(F): 1.34 / Phase error: 29.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2856 471 4.78 %
Rwork0.2184 --
obs0.2215 9850 99.61 %
all-9906 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 79.532 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.1427 Å2-0 Å2-0 Å2
2--7.1427 Å20 Å2
3----14.2854 Å2
Refinement stepCycle: LAST / Resolution: 2.952→44.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1965 0 56 0 2021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012061
X-RAY DIFFRACTIONf_angle_d1.4182806
X-RAY DIFFRACTIONf_dihedral_angle_d23.251736
X-RAY DIFFRACTIONf_chiral_restr0.079305
X-RAY DIFFRACTIONf_plane_restr0.012370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.952-3.3790.32491600.2713011X-RAY DIFFRACTION99
3.379-4.25670.32731500.19463097X-RAY DIFFRACTION100
4.2567-44.92020.25581610.21513271X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 6.6589 Å / Origin y: -23.0921 Å / Origin z: -0.1964 Å
111213212223313233
T0.8218 Å20.1275 Å2-0.0276 Å2-0.1515 Å20.05 Å2--0.2622 Å2
L3.0722 °2-1.2295 °2-0.679 °2-1.572 °21.4125 °2--2.6439 °2
S-0.3424 Å °-0.3726 Å °0.051 Å °0.5593 Å °0.3392 Å °-0.0777 Å °1.1706 Å °0.3064 Å °0.0617 Å °
Refinement TLS groupSelection details: chain A

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