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Basic information

Entry
Database: PDB / ID: 3fhi
TitleCrystal structure of a complex between the catalytic and regulatory (RI{alpha}) subunits of PKA
Components
  • cAMP-dependent protein kinase catalytic subunit alpha
  • cAMP-dependent protein kinase type I-alpha regulatory subunit
KeywordsTRANSFERASE / cAMP / cAMP dependent protein kinase / Protein-Protein complex / AMP-PNP / Protein kinase Regulation / nucleotide binding / protein kinase activity / protein serine/threonine kinase activity / cAMP-dependent protein kinase activity / protein binding / ATP binding / kinase activity / transferase activity / ATP-binding / Kinase / Lipoprotein / Myristate / Nucleotide-binding / Nucleus / Phosphoprotein / Serine/threonine-protein kinase / cAMP-binding
Function / homology
Function and homology information


spontaneous exocytosis of neurotransmitter / negative regulation of meiotic cell cycle / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / HDL assembly / regulation of protein processing / DARPP-32 events / Rap1 signalling / PKA activation / Regulation of insulin secretion ...spontaneous exocytosis of neurotransmitter / negative regulation of meiotic cell cycle / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / HDL assembly / regulation of protein processing / DARPP-32 events / Rap1 signalling / PKA activation / Regulation of insulin secretion / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Vasopressin regulates renal water homeostasis via Aquaporins / Factors involved in megakaryocyte development and platelet production / cellular response to parathyroid hormone stimulus / GPER1 signaling / protein localization to lipid droplet / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Hedgehog 'off' state / Factors involved in megakaryocyte development and platelet production / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / PKA activation / Hedgehog 'off' state / Anchoring of the basal body to the plasma membrane / Recruitment of NuMA to mitotic centrosomes / MAPK6/MAPK4 signaling / AURKA Activation by TPX2 / regulation of cellular respiration / Interleukin-3, Interleukin-5 and GM-CSF signaling / CD209 (DC-SIGN) signaling / RET signaling / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / GLI3 is processed to GLI3R by the proteasome / sperm head-tail coupling apparatus / Regulation of PLK1 Activity at G2/M Transition / Mitochondrial protein degradation / cellular response to cold / VEGFA-VEGFR2 Pathway / nucleotide-activated protein kinase complex / interleukin-2-mediated signaling pathway / Ion homeostasis / mesoderm formation / cAMP-dependent protein kinase inhibitor activity / TORC1 signaling / potassium channel inhibitor activity / histone H1-4S35 kinase activity / cAMP-dependent protein kinase / positive regulation of triglyceride catabolic process / negative regulation of glycolytic process / negative regulation of activated T cell proliferation / cAMP-dependent protein kinase activity / regulation of bicellular tight junction assembly / cAMP-dependent protein kinase complex / neural tube closure / negative regulation of glycolytic process through fructose-6-phosphate / sperm capacitation / regulation of osteoblast differentiation / peptidyl-threonine phosphorylation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / protein kinase A regulatory subunit binding / ciliary base / protein kinase A catalytic subunit binding / intracellular potassium ion homeostasis / immunological synapse / plasma membrane raft / axoneme / cAMP/PKA signal transduction / postsynaptic modulation of chemical synaptic transmission / cAMP binding / regulation of synaptic transmission, glutamatergic / sperm flagellum / positive regulation of gluconeogenesis / negative regulation of cAMP/PKA signal transduction / cellular response to nutrient levels / positive regulation of protein export from nucleus / multivesicular body / negative regulation of TORC1 signaling / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / negative regulation of smoothened signaling pathway / positive regulation of phagocytosis / acrosomal vesicle / sperm midpiece / regulation of proteasomal protein catabolic process / negative regulation of protein localization to chromatin / lipid droplet / cellular response to glucose stimulus / neuromuscular junction / regulation of microtubule cytoskeleton organization / positive regulation of cholesterol biosynthetic process / peptidyl-serine phosphorylation / modulation of chemical synaptic transmission / small GTPase binding / mRNA processing / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway
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. / cAMP-dependent protein kinase catalytic subunit / Cyclic nucleotide-binding domain signature 1. / 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. / cAMP-dependent protein kinase catalytic subunit / 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 / Jelly Rolls / Cyclic nucleotide-binding domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Jelly Rolls / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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 / molecular replacement / Resolution: 2 Å
AuthorsKim, C.
CitationJournal: Science / Year: 2005
Title: Crystal structure of a complex between the catalytic and regulatory (RIalpha) subunits of PKA.
Authors: Kim, C. / Xuong, N.H. / Taylor, S.S.
History
DepositionDec 9, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionApr 14, 2009ID: 1U7E
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.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.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.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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)58,5815
Polymers57,9652
Non-polymers6163
Water2,864159
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-13 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.453, 93.017, 122.043
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 40625.254 Da / Num. of mol.: 1 / Mutation: C199A
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: 17339.561 Da / Num. of mol.: 1 / Fragment: UNP residues 92-245
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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
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: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20 % PEG 2000, 0.1 M Tris-HCl, 4 % 1,3-Propanediol, 2.0 mM Cyclohexyl-pentyl-D-maltoside, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2003
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 42244 / % possible obs: 99.15 % / Observed criterion σ(I): 2 / Redundancy: 23.5 % / Biso Wilson estimate: 34.9 Å2 / Rsym value: 0.076 / Net I/σ(I): 28.3
Reflection shellResolution: 2→2.059 Å / Mean I/σ(I) obs: 2.8 / Rsym value: 0.253 / % possible all: 96.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
DMphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.427 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2136 5.1 %RANDOM
Rwork0.198 ---
obs0.199 42244 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.36 Å2 / Biso mean: 44.572 Å2 / Biso min: 2 Å2 /
Baniso -1Baniso -3
1-0.17 Å2-
2--0 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3842 0 33 159 4034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223966
X-RAY DIFFRACTIONr_bond_other_d0.0010.022661
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9575381
X-RAY DIFFRACTIONr_angle_other_deg0.88436453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1615486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74423.667180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05215645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7011523
X-RAY DIFFRACTIONr_chiral_restr0.0840.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024422
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02861
X-RAY DIFFRACTIONr_nbd_refined0.2230.2806
X-RAY DIFFRACTIONr_nbd_other0.1960.22789
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21956
X-RAY DIFFRACTIONr_nbtor_other0.0870.22041
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2176
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2280.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.28
X-RAY DIFFRACTIONr_mcbond_it0.741.52597
X-RAY DIFFRACTIONr_mcbond_other0.1571.5990
X-RAY DIFFRACTIONr_mcangle_it1.09523867
X-RAY DIFFRACTIONr_scbond_it1.73531735
X-RAY DIFFRACTIONr_scangle_it2.5054.51514
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 144 -
Rwork0.264 2870 -
all-3014 -
obs--99.34 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.45330.32670.14662.43871.20751.8748-0.11270.3550.0602-0.9870.1329-0.0605-0.31780.1779-0.02030.1812-0.08640.02180.174-0.05-0.088719.7243.15429.671
21.55220.0055-0.15441.0946-0.18231.0342-0.05410.19220.0973-0.11340.0324-0.08380.0455-0.03640.0217-0.12-0.0518-0.0110.03160.0271-0.26419.46735.27248.5
315.15689.00398.71546.19152.347614.5148-0.2099-0.1288-0.3546-0.76380.717-0.40870.3891-0.9316-0.50720.2356-0.124-0.04840.3072-0.04450.082312.4136.0436.55
41.18310.2697-0.22871.99080.25551.2963-0.10320.1519-0.1666-0.31730.09980.0369-0.00270.02470.0033-0.1612-0.03080.0263-0.0445-0.0296-0.264619.1384.58648.595
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 128
2X-RAY DIFFRACTION2B92 - 240
3X-RAY DIFFRACTION3A400 - 403
4X-RAY DIFFRACTION4A129 - 350

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