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- PDB-4xw6: X-ray structure of PKAc with ADP, free phosphate ion, CP20, magne... -

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Basic information

Entry
Database: PDB / ID: 4xw6
TitleX-ray structure of PKAc with ADP, free phosphate ion, CP20, magnesium ions
Components(cAMP-dependent protein kinase ...) x 2
KeywordsTRANSFERASE / protein kinase A / ATP hydrolysis / catalytic subunit / ATPase
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 / Vasopressin regulates renal water homeostasis via Aquaporins / 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 / 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 / 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 / cAMP-dependent protein kinase activity / molecular function inhibitor 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 / protein kinase A regulatory subunit binding / ciliary base / protein kinase A catalytic subunit binding / intracellular potassium ion homeostasis / plasma membrane raft / axoneme / cAMP/PKA signal transduction / postsynaptic modulation of chemical synaptic transmission / 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 / 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 / manganese ion binding / protein autophosphorylation / cellular response to heat / presynapse / adenylate cyclase-activating G protein-coupled receptor signaling pathway / molecular adaptor activity / regulation of cell cycle / protein kinase activity / protein phosphorylation / postsynapse / nuclear speck / protein domain specific binding / protein serine kinase activity
Similarity search - Function
cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGerlits, O. / Tian, J. / Das, A. / Taylor, S. / Langan, P. / Heller, T.W. / Kovalevsky, A.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Phosphoryl Transfer Reaction Snapshots in Crystals: INSIGHTS INTO THE MECHANISM OF PROTEIN KINASE A CATALYTIC SUBUNIT.
Authors: Gerlits, O. / Tian, J. / Das, A. / Langan, P. / Heller, W.T. / Kovalevsky, A.
History
DepositionJan 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Jul 1, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_conn.ptnr2_label_seq_id
Revision 1.4Nov 13, 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 inhibitor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3526
Polymers43,7822
Non-polymers5714
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-41 kcal/mol
Surface area15830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.304, 79.228, 97.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 41566.172 Da / Num. of mol.: 1 / Fragment: UNP residues 15-351
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/peptide cAMP-dependent protein kinase inhibitor alpha / PKI-alpha / cAMP-dependent protein kinase inhibitor / muscle/brain isoform


Mass: 2215.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oryctolagus cuniculus (rabbit) / References: UniProt: P61926*PLUS

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Non-polymers , 4 types, 381 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 100 mM MES pH 6.5, 5 mM DTT, 15-20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 32017 / % possible obs: 98.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 30.15
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.5 / % possible all: 91.9

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Processing

Software
NameClassification
PHASERphasing
SHELXrefinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DH3

4dh3


Resolution: 1.9→20 Å / Num. parameters: 11842 / Num. restraintsaints: 12515 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2646 1595 5 %RANDOM
Rwork0.186 32017 --
obs0.186 32017 89.9 %-
Refine analyzeNum. disordered residues: 6 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3302.2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2957 0 65 377 3399
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0305
X-RAY DIFFRACTIONs_zero_chiral_vol0.095
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.096
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.147
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.08
X-RAY DIFFRACTIONs_approx_iso_adps0

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