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- PDB-3of1: Crystal Structure of Bcy1, the Yeast Regulatory Subunit of PKA -

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Basic information

Entry
Database: PDB / ID: 3of1
TitleCrystal Structure of Bcy1, the Yeast Regulatory Subunit of PKA
ComponentscAMP-dependent protein kinase regulatory subunitCAMP-dependent pathway
KeywordsTRANSFERASE / Cyclic nucleotide binding domain / Evolution / PKA signaling / Regulatory subunit / cAMP-dependent protein kinase
Function / homology
Function and homology information


GPER1 signaling / PKA activation / PKA activation in glucagon signalling / DARPP-32 events / Vasopressin regulates renal water homeostasis via Aquaporins / CREB1 phosphorylation through the activation of Adenylate Cyclase / Hedgehog 'off' state / protein localization to bud neck / Factors involved in megakaryocyte development and platelet production / regulation of cytoplasmic mRNA processing body assembly ...GPER1 signaling / PKA activation / PKA activation in glucagon signalling / DARPP-32 events / Vasopressin regulates renal water homeostasis via Aquaporins / CREB1 phosphorylation through the activation of Adenylate Cyclase / Hedgehog 'off' state / protein localization to bud neck / Factors involved in megakaryocyte development and platelet production / regulation of cytoplasmic mRNA processing body assembly / negative regulation of Ras protein signal transduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase complex / protein kinase A catalytic subunit binding / cAMP binding / regulation of protein phosphorylation / chromatin / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / plasma 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
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / cAMP-dependent protein kinase regulatory subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsRinaldi, J. / Wu, J. / Yang, J. / Ralston, C.Y. / Sankaran, B. / Moreno, S. / Taylor, S.S.
CitationJournal: Structure / Year: 2010
Title: Structure of Yeast Regulatory Subunit: A Glimpse into the Evolution of PKA Signaling.
Authors: Rinaldi, J. / Wu, J. / Yang, J. / Ralston, C.Y. / Sankaran, B. / Moreno, S. / Taylor, S.S.
History
DepositionAug 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1763
Polymers27,5171
Non-polymers6582
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)146.425, 45.042, 39.103
Angle α, β, γ (deg.)90.00, 92.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein cAMP-dependent protein kinase regulatory subunit / CAMP-dependent pathway / PKA regulatory subunit


Mass: 27517.494 Da / Num. of mol.: 1 / Fragment: cAMP 1 and cAMP 2 nucleotide binding regions
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BCY1, REG1, SRA1, YIL033C / Production host: Escherichia coli (E. coli) / References: UniProt: P07278
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% polyethylene glycol 3350, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 12845 / Num. obs: 12845 / % possible obs: 91.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.058 / Rsym value: 0.051 / Net I/σ(I): 23.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 3.8 / Num. unique all: 713 / Rsym value: 0.227 / % possible all: 55.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RGS A-domain

1rgs


Resolution: 2.21→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.262 / SU ML: 0.163 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.352 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.263 565 4.8 %RANDOM
Rwork0.2 ---
obs0.2 11232 91.4 %-
all-12845 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.627 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å2-0 Å2-0.37 Å2
2---0.7 Å20 Å2
3----1.7 Å2
Refinement stepCycle: LAST / Resolution: 2.21→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1820 0 44 93 1957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221901
X-RAY DIFFRACTIONr_angle_refined_deg2.21.9942591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8855245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.36924.875
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.80915291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.236158
X-RAY DIFFRACTIONr_chiral_restr0.1620.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021426
X-RAY DIFFRACTIONr_nbd_refined0.2410.2817
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21282
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2119
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.27
X-RAY DIFFRACTIONr_mcbond_it1.2871.51249
X-RAY DIFFRACTIONr_mcangle_it2.16521929
X-RAY DIFFRACTIONr_scbond_it3.2743754
X-RAY DIFFRACTIONr_scangle_it4.6014.5662
LS refinement shellResolution: 2.21→2.267 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 26 -
Rwork0.213 441 -
obs--49.84 %

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