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- PDB-4wb8: Crystal structure of human cAMP-dependent protein kinase A (catal... -

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Basic information

Entry
Database: PDB / ID: 4wb8
TitleCrystal structure of human cAMP-dependent protein kinase A (catalytic alpha subunit), exon 1 deletion
Components
  • PKI (5-24)
  • cAMP-dependent protein kinase catalytic subunit alphaCAMP-dependent pathway
KeywordsTRANSFERASE/TRANSFERASE Inhibitor / catalysis / protein kinase / adenosine triphosphate / phosphorylation / TRANSFERASE-TRANSFERASE Inhibitor complex
Function / homology
Function and homology information


PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / mitochondrial protein catabolic process / ROBO receptors bind AKAP5 / HDL assembly / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / negative regulation of cAMP-dependent protein kinase activity / regulation of protein binding / nucleotide-activated protein kinase complex / high-density lipoprotein particle assembly ...PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / mitochondrial protein catabolic process / ROBO receptors bind AKAP5 / HDL assembly / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / negative regulation of cAMP-dependent protein kinase activity / regulation of protein binding / nucleotide-activated protein kinase complex / high-density lipoprotein particle assembly / Rap1 signalling / renal water homeostasis / regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cell communication by electrical coupling involved in cardiac conduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / Loss of phosphorylation of MECP2 at T308 / sperm capacitation / regulation of osteoblast differentiation / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / cAMP-dependent protein kinase activity / ciliary base / cAMP-dependent protein kinase complex / negative regulation of glycolytic process through fructose-6-phosphate / AMP-activated protein kinase activity / negative regulation of protein import into nucleus / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / Triglyceride catabolism / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / plasma membrane raft / PKA activation in glucagon signalling / : / Regulation of MECP2 expression and activity / mesoderm formation / regulation of cardiac conduction / RET signaling / DARPP-32 events / Interleukin-3, Interleukin-5 and GM-CSF signaling / sperm flagellum / Mitochondrial protein degradation / regulation of macroautophagy / regulation of cardiac muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Hedgehog 'off' state / negative regulation of smoothened signaling pathway / regulation of proteasomal protein catabolic process / positive regulation of gluconeogenesis / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / sperm midpiece / negative regulation of TORC1 signaling / protein kinase A signaling / Recruitment of NuMA to mitotic centrosomes / cellular response to epinephrine stimulus / calcium channel complex / Anchoring of the basal body to the plasma membrane / regulation of cytosolic calcium ion concentration / regulation of G2/M transition of mitotic cell cycle / protein export from nucleus / protein serine/threonine/tyrosine kinase activity / regulation of heart rate / CD209 (DC-SIGN) signaling / AURKA Activation by TPX2 / FCGR3A-mediated IL10 synthesis / positive regulation of protein export from nucleus / acrosomal vesicle / Regulation of insulin secretion / neural tube closure / cellular response to glucose stimulus / Degradation of GLI1 by the proteasome / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / Vasopressin regulates renal water homeostasis via Aquaporins / cytokine-mediated signaling pathway / VEGFA-VEGFR2 Pathway / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / Regulation of PLK1 Activity at G2/M Transition / cellular response to heat / manganese ion binding / Factors involved in megakaryocyte development and platelet production / peptidyl-serine phosphorylation / dendritic spine / regulation of cell cycle
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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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'-TRIPHOSPHATE / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsCheung, J. / Ginter, C. / Cassidy, M. / Franklin, M.C. / Rudolph, M.J. / Hendrickson, W.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural insights into mis-regulation of protein kinase A in human tumors.
Authors: Cheung, J. / Ginter, C. / Cassidy, M. / Franklin, M.C. / Rudolph, M.J. / Robine, N. / Darnell, R.B. / Hendrickson, W.A.
History
DepositionSep 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Feb 11, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.4Sep 27, 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 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cAMP-dependent protein kinase catalytic subunit alpha
I: PKI (5-24)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4606
Polymers41,7092
Non-polymers7514
Water9,278515
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-20 kcal/mol
Surface area15920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.808, 75.864, 80.644
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AI

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


Mass: 39483.023 Da / Num. of mol.: 1 / Fragment: UNP residues 16-351 / Mutation: none
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKACA, PKACA / Plasmid: pLATE11 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: P17612, cAMP-dependent protein kinase
#2: Protein/peptide PKI (5-24)


Mass: 2226.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P61925*PLUS

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Non-polymers , 4 types, 519 molecules

#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10% PEG 8000, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9795 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 25, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 65054 / % possible obs: 99 % / Redundancy: 5.6 % / Biso Wilson estimate: 19.69 Å2 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.023 / Rrim(I) all: 0.055 / Χ2: 0.874 / Net I/av σ(I): 31.205 / Net I/σ(I): 11.7 / Num. measured all: 363415
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.584.60.66729480.7630.3250.7450.73291.1
1.58-1.614.80.630130.8190.2860.6680.72493.3
1.61-1.645.10.56231770.8020.2690.6270.7298.5
1.64-1.675.30.52632360.8210.2530.5870.73199.6
1.67-1.715.50.43632350.8690.2080.4850.72799.9
1.71-1.755.70.37432430.9120.1760.4150.74100
1.75-1.795.70.31632800.9360.1470.350.754100
1.79-1.845.80.26132330.9580.1220.2890.782100
1.84-1.895.80.24732520.9710.1140.2730.823100
1.89-1.955.80.16632620.9780.0770.1831.015100
1.95-2.025.80.13332710.9870.0610.1470.811100
2.02-2.15.80.09532810.9930.0440.1050.814100
2.1-2.25.80.07732520.9960.0360.0850.857100
2.2-2.325.80.0833020.9940.0370.0891.215100
2.32-2.465.80.05132760.9980.0240.0570.884100
2.46-2.655.80.04333040.9980.020.0480.892100
2.65-2.925.80.03633230.9990.0160.0390.91100
2.92-3.345.80.02933040.9990.0130.0310.973100
3.34-4.215.70.02733860.9980.0120.0291.134100
4.21-505.50.02734760.9980.0120.0291.09298.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GFC

2gfc


Resolution: 1.55→35.274 Å / FOM work R set: 0.8822 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1844 3320 5.11 %RANDOM
Rwork0.1631 61653 --
obs0.1642 64973 99.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.43 Å2 / Biso mean: 28.52 Å2 / Biso min: 11.37 Å2
Refinement stepCycle: final / Resolution: 1.55→35.274 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 0 45 515 3504
Biso mean--28.73 38.77 -
Num. residues----357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113115
X-RAY DIFFRACTIONf_angle_d1.3354222
X-RAY DIFFRACTIONf_chiral_restr0.067438
X-RAY DIFFRACTIONf_plane_restr0.007534
X-RAY DIFFRACTIONf_dihedral_angle_d14.4111171
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.57060.2159970.21462302239990
1.5706-1.59410.24771370.20492395253293
1.5941-1.6190.2631250.19482510263596
1.619-1.64550.2121380.19562508264699
1.6455-1.67390.19571370.193525462683100
1.6739-1.70430.20991510.177625422693100
1.7043-1.73710.22141190.185125892708100
1.7371-1.77260.22131550.195425512706100
1.7726-1.81110.20221280.187926092737100
1.8111-1.85320.25111290.187325492678100
1.8532-1.89960.27291230.206725852708100
1.8996-1.95090.20541710.198925542725100
1.9509-2.00830.17751690.172325592728100
2.0083-2.07310.18431460.16525832729100
2.0731-2.14720.20581200.163125912711100
2.1472-2.23320.23371410.169125872728100
2.2332-2.33480.19541330.185125892722100
2.3348-2.45790.17261340.153426122746100
2.4579-2.61180.16881360.156226032739100
2.6118-2.81340.18871430.157226182761100
2.8134-3.09640.17341440.160726212765100
3.0964-3.54410.1581650.158126072772100
3.5441-4.46370.14821420.136226772819100
4.4637-35.2830.18231370.1482766290398
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)
11.8999-0.72990.76771.57870.27883.22980.11070.0047-0.0365-0.06-0.1140.28880.0148-0.5250.0740.1490.01470.01210.24120.0090.211137.411210.9649-9.1906
23.9279-0.472-2.65881.53380.36273.48480.047-0.12130.42820.12380.05190.121-0.3846-0.2096-0.07440.20640.054-0.02540.1632-0.03930.175343.123819.6303-0.37
30.8428-0.11380.03210.9718-0.40961.3511-0.0179-0.0556-0.01720.0530.02480.148-0.0316-0.2283-0.0170.14210.01710.00430.1886-0.03350.165542.30494.4101-2.2133
41.85320.14890.09331.6662-0.72792.64460.01170.0887-0.0997-0.0519-0.04970.06750.0765-0.10130.04430.11040.0179-0.01130.1424-0.02490.124946.34041.3924-6.4217
51.9820.4246-0.1332.1126-1.36353.31590.0402-0.0456-0.1933-0.0308-0.1378-0.16060.33120.34350.09310.180.05730.00810.172-0.00660.164656.5475-9.8360.0583
64.4661-0.1449-0.31142.6684-0.19182.33760.0320.1379-0.5435-0.1288-0.05880.35530.4789-0.34870.04890.2642-0.0677-0.03130.1959-0.0060.219440.2765-13.8016-3.228
70.7882-0.0956-0.3033.6781-2.67796.18580.0145-0.09730.24240.45560.0614-0.0515-0.7329-0.1253-0.09470.22960.0802-0.03320.1807-0.04820.237646.102219.87911.5586
83.0059-1.48293.00864.3407-6.26119.39130.0862-0.0972-0.12510.035-0.07140.43460.06440.10390.04450.19320.03030.0010.2458-0.00980.170759.932-8.081215.9897
93.9398-1.07831.5766.49441.42753.5257-0.13060.26870.2137-0.1767-0.1271-0.3094-0.29030.29720.18450.1070.0068-0.00570.19250.01560.120758.82384.0184.0606
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 55 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 81 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 160 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 161 through 198 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 199 through 272 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 273 through 316 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 317 through 350 )A0
8X-RAY DIFFRACTION8chain 'I' and (resid 5 through 11 )I0
9X-RAY DIFFRACTION9chain 'I' and (resid 12 through 24 )I0

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