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- PDB-4mx3: Crystal Structure of PKA RIalpha Homodimer -

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Basic information

Entry
Database: PDB / ID: 4mx3
TitleCrystal Structure of PKA RIalpha Homodimer
ComponentscAMP-dependent protein kinase type I-alpha regulatory subunitCAMP-dependent pathway
KeywordsSIGNALING PROTEIN / PKA / RIalpha Homodimer / Cooperative cAMP Binding / Carney Complex Disease
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 / 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 type I-alpha regulatory subunit
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.88 Å
AuthorsBruystens, J.G.H. / Wu, J. / Fortezzo, A. / Kornev, A.P. / Blumenthal, D.A. / Taylor, S.S.
CitationJournal: Structure / Year: 2014
Title: PKA RI alpha Homodimer Structure Reveals an Intermolecular Interface with Implications for Cooperative cAMP Binding and Carney Complex Disease.
Authors: Bruystens, J.G. / Wu, J. / Fortezzo, A. / Kornev, A.P. / Blumenthal, D.K. / Taylor, S.S.
History
DepositionSep 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: 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
B: cAMP-dependent protein kinase type I-alpha regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9506
Polymers85,6332
Non-polymers1,3174
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: cAMP-dependent protein kinase type I-alpha regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4753
Polymers42,8161
Non-polymers6582
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: cAMP-dependent protein kinase type I-alpha regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4753
Polymers42,8161
Non-polymers6582
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.672, 104.672, 218.327
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A121 - 184
2112B121 - 184
1122A188 - 303
2122B188 - 303
1134A310 - 373
2134B310 - 373
1141A401 - 601
2141B401 - 601

NCS ensembles :
ID
1
2
3
4

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Components

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


Mass: 42816.422 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) / Strain (production host): BL21 / References: UniProt: P00514
#2: Chemical
ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate


Mass: 329.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N5O6P

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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: 3.49 Å3/Da / Density % sol: 64.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.125 M sodium acetate (pH 5), 2M sodium formate with the protein at a final concentration of 4 mg/ml grown in a 2 ul drop, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 19, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.88→50 Å / Num. all: 11872 / Num. obs: 11860 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Redundancy: 9 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 35.9
Reflection shellResolution: 3.88→4.02 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 6.2 / Num. unique all: 1145 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RGS

1rgs


Resolution: 3.88→50 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.892 / SU B: 35.148 / SU ML: 0.492 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.706 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28671 549 4.8 %RANDOM
Rwork0.25954 ---
obs0.26082 11007 97.67 %-
all-11860 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 137.557 Å2
Baniso -1Baniso -2Baniso -3
1-6.28 Å20 Å20 Å2
2--6.28 Å20 Å2
3----12.55 Å2
Refinement stepCycle: LAST / Resolution: 3.88→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4129 0 88 0 4217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224310
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.9925860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8725539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.26524.421190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.79115689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.551526
X-RAY DIFFRACTIONr_chiral_restr0.10.2653
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213262
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1256TIGHT POSITIONAL0.10.05
1242MEDIUM POSITIONAL0.220.5
2464TIGHT POSITIONAL0.080.05
2438MEDIUM POSITIONAL0.150.5
3483MEDIUM POSITIONAL0.720.5
444TIGHT POSITIONAL0.060.05
LS refinement shellResolution: 3.883→3.984 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 41 -
Rwork0.395 761 -
obs--94.24 %

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