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- PDB-3pvb: Crystal structure of (73-244)RIa:C holoenzyme of cAMP-dependent P... -

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Basic information

Entry
Database: PDB / ID: 3pvb
TitleCrystal structure of (73-244)RIa:C holoenzyme of cAMP-dependent Protein kinase
Components(cAMP-dependent protein kinase ...) x 2
KeywordsTRANSFERASE / Kinase / RIa Holoenzyme / Tetrameric Protein Kinase A
Function / homology
Function and homology information


sperm head-tail coupling apparatus / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Regulation of insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Hedgehog 'off' state ...sperm head-tail coupling apparatus / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Regulation of insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Hedgehog 'off' state / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / MAPK6/MAPK4 signaling / AURKA Activation by TPX2 / GLI3 is processed to GLI3R by the proteasome / PKA activation / Factors involved in megakaryocyte development and platelet production / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Regulation of PLK1 Activity at G2/M Transition / Interleukin-3, Interleukin-5 and GM-CSF signaling / CD209 (DC-SIGN) signaling / nucleotide-activated protein kinase complex / Hedgehog 'off' state / RET signaling / Ion homeostasis / Mitochondrial protein degradation / VEGFA-VEGFR2 Pathway / negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / regulation of protein processing / cardiac muscle cell proliferation / cAMP-dependent protein kinase activity / protein localization to lipid droplet / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / sarcomere organization / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / protein kinase A regulatory subunit binding / negative regulation of activated T cell proliferation / protein kinase A catalytic subunit binding / cAMP/PKA signal transduction / mesoderm formation / sperm flagellum / immunological synapse / plasma membrane raft / axoneme / postsynaptic modulation of chemical synaptic transmission / cAMP binding / regulation of proteasomal protein catabolic process / negative regulation of TORC1 signaling / sperm midpiece / negative regulation of smoothened signaling pathway / positive regulation of gluconeogenesis / multivesicular body / cellular response to glucagon stimulus / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / acrosomal vesicle / positive regulation of protein export from nucleus / neural tube closure / modulation of chemical synaptic transmission / positive regulation of cholesterol biosynthetic process / cellular response to glucose stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / manganese ion binding / cellular response to heat / peptidyl-serine phosphorylation / regulation of cell cycle / protein kinase activity / postsynapse / nuclear speck / protein domain specific binding / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ubiquitin protein ligase binding / protein kinase binding
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. / cAMP-dependent protein kinase catalytic subunit / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain ...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. / cAMP-dependent protein kinase catalytic subunit / 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 / Extension to Ser/Thr-type protein kinases / Jelly Rolls / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Jelly Rolls / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / cAMP-dependent protein kinase type I-alpha regulatory subunit / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsBoettcher, A.J. / Wu, J. / Kim, C. / Yang, J. / Bruystens, J. / Cheung, N. / Pennypacker, J.K. / Blumenthal, D.A. / Kornev, A.P. / Taylor, S.S.
CitationJournal: Structure / Year: 2011
Title: Crystal structure of (73-244)RIa:C holoenzyme of cAMP-dependent Protein kinase
Authors: Boettcher, A.J. / Wu, J. / Kim, C. / Yang, J. / Bruystens, J. / Cheung, N. / Pennypacker, J.K. / Blumenthal, D.A. / Kornev, A.P. / Taylor, S.S.
History
DepositionDec 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,0506
Polymers58,3422
Non-polymers7084
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-15 kcal/mol
Surface area22070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.667, 116.667, 140.103
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Detailsone molecule per asymmetrical unit

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Components

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CAMP-dependent protein kinase ... , 2 types, 2 molecules AB

#1: Protein cAMP-dependent protein kinase catalytic subunit alpha / PKA C-alpha


Mass: 40432.891 Da / Num. of mol.: 1 / Fragment: unp residues 7-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prkaca, Pkaca / Production host: Escherichia coli (E. coli) / References: UniProt: P05132, cAMP-dependent protein kinase
#2: Protein cAMP-dependent protein kinase type I-alpha regulatory subunit


Mass: 17909.275 Da / Num. of mol.: 1 / Fragment: unp residues 85-244
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: PRKAR1A / Production host: Escherichia coli (E. coli) / References: UniProt: P00514

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Non-polymers , 4 types, 19 molecules

#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 4.86 Å3/Da / Density % sol: 74.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: The RIa(73-244):C complex was crystallized in 0.1M MES pH 6.0 and 12% PEG 20,000 by using a Douglas Instruments Oryx8 crystallography robot as 1:1 protein solution:crystallizing solution, ...Details: The RIa(73-244):C complex was crystallized in 0.1M MES pH 6.0 and 12% PEG 20,000 by using a Douglas Instruments Oryx8 crystallography robot as 1:1 protein solution:crystallizing solution, VAPOR DIFFUSION, SITTING DROP, temperature 298.0 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 27860 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 19.3
Reflection shellResolution: 3.3→3.39 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1797 / % possible all: 93.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2QCS

2qcs


Resolution: 3.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 --RANDOM
Rwork0.242 ---
obs-27860 97.1 %-
Refinement stepCycle: LAST / Resolution: 3.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3992 0 39 15 4046
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6

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