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- PDB-2izy: Molecular Basis of AKAP Specificity for PKA Regulatory Subunits -

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Basic information

Entry
Database: PDB / ID: 2izy
TitleMolecular Basis of AKAP Specificity for PKA Regulatory Subunits
ComponentsCAMP-DEPENDENT PROTEIN KINASE REGULATORY SUBUNIT II
KeywordsTRANSFERASE / D/D / RII / PKA / CAMP / KINASE / ACETYLATION / CAMP- BINDING / PHOSPHORYLATION / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


GPER1 signaling / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / DARPP-32 events / Factors involved in megakaryocyte development and platelet production / Hedgehog 'off' state / PKA activation / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / DARPP-32 events ...GPER1 signaling / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / DARPP-32 events / Factors involved in megakaryocyte development and platelet production / Hedgehog 'off' state / PKA activation / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / DARPP-32 events / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / GPER1 signaling / Hedgehog 'off' state / Factors involved in megakaryocyte development and platelet production / cAMP-dependent protein kinase regulator activity / nucleotide-activated protein kinase complex / Vasopressin regulates renal water homeostasis via Aquaporins / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase complex / plasma membrane raft / protein kinase A catalytic subunit binding / small molecule binding / beta-2 adrenergic receptor binding / cAMP binding / T-tubule / regulation of protein phosphorylation / modulation of chemical synaptic transmission / protein domain specific binding / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / synapse / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex / identical protein binding / plasma membrane / cytoplasm / cytosol
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
cAMP-dependent protein kinase type II-alpha regulatory subunit / cAMP-dependent protein kinase type II-alpha regulatory subunit
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsGold, M.G. / Lygren, B. / Dokurno, P. / Hoshi, N. / McConnachie, G. / Tasken, K. / Carlson, C.R. / Scott, J.D. / Barford, D.
CitationJournal: Mol.Cell / Year: 2006
Title: Molecular Basis of Akap Specificity for Pka Regululatory Subunits
Authors: Gold, M.G. / Lygren, B. / Dokurno, P. / Hoshi, N. / Mcconnachie, G. / Tasken, K. / Carlson, C.R. / Scott, J.D. / Barford, D.
History
DepositionJul 27, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CAMP-DEPENDENT PROTEIN KINASE REGULATORY SUBUNIT II
B: CAMP-DEPENDENT PROTEIN KINASE REGULATORY SUBUNIT II
C: CAMP-DEPENDENT PROTEIN KINASE REGULATORY SUBUNIT II
D: CAMP-DEPENDENT PROTEIN KINASE REGULATORY SUBUNIT II
E: CAMP-DEPENDENT PROTEIN KINASE REGULATORY SUBUNIT II
F: CAMP-DEPENDENT PROTEIN KINASE REGULATORY SUBUNIT II
G: CAMP-DEPENDENT PROTEIN KINASE REGULATORY SUBUNIT II
H: CAMP-DEPENDENT PROTEIN KINASE REGULATORY SUBUNIT II


Theoretical massNumber of molelcules
Total (without water)51,1068
Polymers51,1068
Non-polymers00
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.490, 91.490, 189.047
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-2022-

HOH

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Components

#1: Protein
CAMP-DEPENDENT PROTEIN KINASE REGULATORY SUBUNIT II


Mass: 6388.239 Da / Num. of mol.: 8 / Fragment: RESIDUES 2-44
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET20 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P12368, UniProt: P12367*PLUS, cAMP-dependent protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growpH: 5.8
Details: 8-10% PEG400, 0.2-0.4 M SODIUM PHOSPHATE AND SODIUM CITRATE (PH 5.8)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 8, 2000 / Details: MIRROR
RadiationMonochromator: SILICON / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 23415 / % possible obs: 100 % / Observed criterion σ(I): 2.5 / Redundancy: 28 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.6
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.24 / % possible all: 88.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→29.58 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.879 / SU B: 5.517 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.306 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES VISIBLE C-TERMINAL TO POSITION 46 ARE PART OF AN UNCLEAVED 6HIS TAG
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1970 8.4 %RANDOM
Rwork0.215 ---
obs0.22 21445 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3010 0 0 270 3280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223074
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.9954186
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.665366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.86422.875160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.17215491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6121537
X-RAY DIFFRACTIONr_chiral_restr0.0870.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022401
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.21445
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22113
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2194
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7271.51942
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22423026
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.80331267
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9424.51160
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.314 112
Rwork0.205 1267

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