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- PDB-1rl3: Crystal structure of cAMP-free R1a subunit of PKA -

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Basic information

Entry
Database: PDB / ID: 1rl3
TitleCrystal structure of cAMP-free R1a subunit of PKA
ComponentscAMP-dependent protein kinase type I-alpha regulatory chain
KeywordsKINASE / Type 1a regulatory subunit / cAMP-dependent protein kinase / cAMP-free
Function / homology
Function and homology information


: / 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 ...: / 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 / Vasopressin regulates renal water homeostasis via Aquaporins / sarcomere organization / cellular response to glucagon stimulus / negative regulation of activated T cell proliferation / plasma membrane raft / protein kinase A catalytic subunit binding / axoneme / immunological synapse / mesoderm formation / cAMP binding / multivesicular body / regulation of protein phosphorylation / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / protein domain specific binding / negative regulation of gene expression / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / identical protein binding / cytoplasm / cytosol
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 speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsWu, J. / Brown, S. / Xuong, N.-H. / Taylor, S.S.
CitationJournal: Structure / Year: 2004
Title: RIalpha subunit of PKA: a cAMP-free structure reveals a hydrophobic capping mechanism for docking cAMP into site B.
Authors: Wu, J. / Brown, S. / Xuong, N.H. / Taylor, S.S.
History
DepositionNov 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 23, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,9547
Polymers64,9882
Non-polymers9675
Water30617
1
A: cAMP-dependent protein kinase type I-alpha regulatory chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9313
Polymers32,4941
Non-polymers4372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cAMP-dependent protein kinase type I-alpha regulatory chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0234
Polymers32,4941
Non-polymers5293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.3, 90.3, 177.6
Angle α, β, γ (deg.)90, 90, 120
Int Tables number170
Space group name H-MP65

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Components

#1: Protein cAMP-dependent protein kinase type I-alpha regulatory chain


Mass: 32493.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: PRKAR1A / Production host: Escherichia coli (E. coli) / References: UniProt: P00514
#2: Chemical ChemComp-PCG / CYCLIC GUANOSINE MONOPHOSPHATE


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: NH4SO4, glycerol, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.5K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 17, 2002
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 22489 / Num. obs: 21075 / % possible obs: 93.7 % / Observed criterion σ(F): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.053
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2495 / % possible all: 93.1

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1RGS

1rgs


Resolution: 2.7→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.285 1642 random
Rwork0.24 --
all-22489 -
obs-21075 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.13 Å211.15 Å20 Å2
2---5.13 Å20 Å2
3---10.26 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3927 0 64 17 4008
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d1.18
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.043 /
RfactorNum. reflection
Rfree0.418 95
Rwork0.345 -
obs-896

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