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- PDB-3im3: Crystal structure of PKA RI alpha dimerization/docking domain -

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Basic information

Entry
Database: PDB / ID: 3im3
TitleCrystal structure of PKA RI alpha dimerization/docking domain
ComponentscAMP-dependent protein kinase type I-alpha regulatory subunitCAMP-dependent pathway
KeywordsSTRUCTURAL PROTEIN / SIGNALING PROTEIN / helix-turn-helix / Acetylation / cAMP / cAMP-binding / Disulfide bond / Nucleotide-binding / Phosphoprotein
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 / Hedgehog 'off' state / nucleotide-activated protein kinase complex / 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 / Hedgehog 'off' state / nucleotide-activated protein kinase complex / cAMP-dependent protein kinase inhibitor activity / sarcomere organization / cardiac muscle cell proliferation / cAMP-dependent protein kinase complex / 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 / 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 / cytosol / cytoplasm
Similarity search - Function
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 / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate 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 / 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 / RmlC-like jelly roll fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
FORMIC ACID / cAMP-dependent protein kinase type I-alpha regulatory subunit
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSarma, G.N. / Kinderman, F.S. / Kim, C. / von Daake, S. / Taylor, S.S.
CitationJournal: Structure / Year: 2010
Title: Structure of D-AKAP2:PKA RI Complex: Insights into AKAP Specificity and Selectivity
Authors: Sarma, G.N. / Kinderman, F.S. / Kim, C. / von Daake, S. / Chen, L. / Wang, B.C. / Taylor, S.S.
History
DepositionAug 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 7, 2021Group: Derived calculations / Category: struct_site
Item: _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)6,0983
Polymers6,0061
Non-polymers922
Water52229
1
A: cAMP-dependent protein kinase type I-alpha regulatory subunit
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)12,1966
Polymers12,0122
Non-polymers1844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area2450 Å2
ΔGint-27 kcal/mol
Surface area7370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.122, 44.122, 93.036
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-118-

HOH

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Components

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


Mass: 6005.980 Da / Num. of mol.: 1
Fragment: Dimerization and docking domain: UNP residues 13-62
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: PRKAR1A / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00514
#2: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.18 Å3/Da / Density % sol: 43.48 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 9
Details: 30% PEG 3350, 0.2 mM Sodium formate, 0.1 M Bis-Tris propane pH 9.0, MICROBATCH, temperature 298K

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 4047 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 36.9 %
Reflection shellResolution: 2→2.07 Å / Redundancy: 27.6 % / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
SOLVEphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→24.0811 Å / SU ML: 0.26 / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 387 9.85 %Random
Rwork0.1871 ---
all0.193 3929 --
obs0.193 3929 97.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.312 Å2 / ksol: 0.351 e/Å3
Refinement stepCycle: LAST / Resolution: 2→24.0811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms428 0 6 29 463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006441
X-RAY DIFFRACTIONf_angle_d0.835588
X-RAY DIFFRACTIONf_dihedral_angle_d14.452178
X-RAY DIFFRACTIONf_chiral_restr0.05564
X-RAY DIFFRACTIONf_plane_restr0.00476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.28940.24841200.18411113X-RAY DIFFRACTION96
2.2894-2.88360.27291270.16991147X-RAY DIFFRACTION98
2.8836-24.08110.23841400.19331282X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 17.8277 Å / Origin y: -0.4668 Å / Origin z: -11.5683 Å
111213212223313233
T0.1501 Å2-0.0325 Å20.0263 Å2-0.258 Å20.0282 Å2--0.2215 Å2
L0.7044 °20.2591 °20.6056 °2-2.9855 °2-0.9891 °2--1.9343 °2
S-0.0432 Å °-0.0432 Å °0.027 Å °0.1256 Å °0.2525 Å °0.3979 Å °0.0611 Å °-0.3353 Å °-0.1415 Å °
Refinement TLS groupSelection details: chain A

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