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- PDB-4wb5: Crystal structure of human cAMP-dependent protein kinase A (catal... -

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Basic information

Entry
Database: PDB / ID: 4wb5
TitleCrystal structure of human cAMP-dependent protein kinase A (catalytic alpha subunit)
Components
  • PKI (5-24)
  • cAMP-dependent protein kinase catalytic subunit alpha
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 / ROBO receptors bind AKAP5 / HDL assembly / mitochondrial protein catabolic process / 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 / ROBO receptors bind AKAP5 / HDL assembly / mitochondrial protein catabolic process / 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 / regulation of osteoblast differentiation / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / sperm capacitation / cAMP-dependent protein kinase activity / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / cAMP-dependent protein kinase complex / 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 / plasma membrane raft / protein kinase A catalytic subunit binding / PKA activation in glucagon signalling / : / Regulation of MECP2 expression and activity / mesoderm formation / RET signaling / DARPP-32 events / Interleukin-3, Interleukin-5 and GM-CSF signaling / regulation of cardiac muscle contraction / regulation of cardiac conduction / sperm flagellum / regulation of macroautophagy / 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 / 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 / positive regulation of gluconeogenesis / Recruitment of mitotic centrosome proteins and complexes / sperm midpiece / negative regulation of TORC1 signaling / Recruitment of NuMA to mitotic centrosomes / protein kinase A signaling / Mitochondrial protein degradation / calcium channel complex / Anchoring of the basal body to the plasma membrane / cellular response to epinephrine stimulus / regulation of cytosolic calcium ion concentration / regulation of G2/M transition of mitotic cell cycle / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / 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 / neural tube closure / Regulation of insulin secretion / 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 / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / mRNA processing / cytokine-mediated signaling pathway / VEGFA-VEGFR2 Pathway / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / Regulation of PLK1 Activity at G2/M Transition / Factors involved in megakaryocyte development and platelet production / cellular response to heat / manganese ion binding / 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: 1.641 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 1.3Feb 25, 2015Group: Derived calculations
Revision 1.4Nov 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 1.5Sep 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.d_res_high / _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)43,5405
Polymers42,9842
Non-polymers5563
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-25 kcal/mol
Surface area15990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.178, 75.091, 80.716
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: 40757.352 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-ATP / ADENOSINE-5'-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10% PEG 6000, 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: 1.641→50 Å / Num. obs: 54512 / % possible obs: 99.8 % / Redundancy: 5.4 % / Biso Wilson estimate: 23.24 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.026 / Rrim(I) all: 0.062 / Χ2: 0.946 / Net I/av σ(I): 30.98 / Net I/σ(I): 10.6 / Num. measured all: 294985
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.641-1.684.70.84627070.5870.4310.9530.79899.9
1.68-1.715.20.86826850.7520.4160.9650.587100
1.71-1.745.30.72626670.7970.3470.8060.609100
1.74-1.785.30.61126820.8610.2910.6780.621100
1.78-1.825.40.47927330.90.2260.5310.639100
1.82-1.865.40.4126770.9310.1930.4540.66499.9
1.86-1.95.40.32126930.950.1510.3550.697100
1.9-1.965.50.26327090.960.1240.2920.791100
1.96-2.015.50.19527180.9770.0910.2160.724100
2.01-2.085.50.15426920.9840.0720.1710.803100
2.08-2.155.50.11927290.9910.0560.1310.822100
2.15-2.245.50.09727340.9930.0450.1070.874100
2.24-2.345.50.0926980.9940.0420.0991.075100
2.34-2.465.50.06827320.9960.0320.0760.971100
2.46-2.625.60.0627370.9970.0280.0660.98899.9
2.62-2.825.50.05127330.9970.0240.0571.07999.9
2.82-3.115.50.04427610.9980.0210.0481.26999.7
3.11-3.555.50.03527490.9980.0170.0391.54399.4
3.55-4.485.50.03127820.9980.0150.0341.71299
4.48-505.30.03228940.9980.0150.0351.49997.8

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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: 4WB8

4wb8


Resolution: 1.641→36.589 Å / FOM work R set: 0.8588 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1956 2641 4.85 %RANDOM
Rwork0.1633 51814 --
obs0.165 54455 98.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.35 Å2 / Biso mean: 31.54 Å2 / Biso min: 13.25 Å2
Refinement stepCycle: final / Resolution: 1.641→36.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2955 0 33 405 3393
Biso mean--21.58 40.49 -
Num. residues----358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123162
X-RAY DIFFRACTIONf_angle_d1.3724295
X-RAY DIFFRACTIONf_chiral_restr0.073449
X-RAY DIFFRACTIONf_plane_restr0.007548
X-RAY DIFFRACTIONf_dihedral_angle_d14.1741187
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.641-1.67080.33541080.24852267237583
1.6708-1.7030.28791340.231627142848100
1.703-1.73770.20391250.20627392864100
1.7377-1.77550.23941350.19727142849100
1.7755-1.81680.2391340.186927332867100
1.8168-1.86220.23351450.19227062851100
1.8622-1.91260.27311300.198427472877100
1.9126-1.96890.21311420.184627522894100
1.9689-2.03240.20821110.170927672878100
2.0324-2.1050.18111190.16227292848100
2.105-2.18930.19771250.161427562881100
2.1893-2.28890.20761530.165627412894100
2.2889-2.40960.19471410.164827432884100
2.4096-2.56050.21491700.168227122882100
2.5605-2.75820.22631630.172927632926100
2.7582-3.03560.22771500.170327562906100
3.0356-3.47460.18711520.16327842936100
3.4746-4.37650.17141530.13622796294999
4.3765-36.59810.14831510.14692895304698
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)
17.945-4.68790.9983.72-1.71843.4917-0.0135-0.29650.29660.71860.10310.5797-0.6046-0.8347-0.0630.3270.0670.08480.3562-0.0430.3154-40.15741.355718.0822
21.4493-0.5108-1.61051.0902-0.9254.5148-0.0496-0.0649-0.0554-0.1106-0.00350.03650.47840.09740.02830.2343-0.09930.00280.261-0.03870.2849-32.033-20.16751.2502
34.17480.01412.87992.245-0.04114.6404-0.0340.2152-0.2331-0.14540.06930.14060.3476-0.1017-0.02390.1752-0.04480.02580.1896-0.03440.183-30.375-19.44870.0881
40.72420.1534-0.03961.5446-0.57622.0876-0.04820.0862-0.0045-0.07410.0710.1836-0.0353-0.2902-0.04920.1181-0.0054-0.01220.1955-0.02470.1764-30.6238-4.33531.9636
51.03320.4809-0.40222.0481-1.10293.46870.0072-0.08430.02140.0122-0.1332-0.1173-0.17530.25020.12890.13810.0074-0.0060.1496-0.00720.1372-19.6023.1813.7593
62.7110.42570.39462.6766-0.90034.148-0.0254-0.10780.42570.2416-0.0327-0.0216-0.89480.05110.03440.46540.0034-0.01320.1498-0.01040.27-23.067318.24422.8453
70.65370.5658-0.48873.79991.52592.33020.0360.3050.1586-0.4321-0.10820.7188-0.2927-0.59610.06530.31610.1598-0.0940.45840.0370.3992-41.42888.9881-3.4718
80.54970.0760.59814.2686-2.91066.5301-0.00110.1205-0.1858-0.46540.0273-0.09940.722-0.0488-0.10970.1852-0.05890.04160.2226-0.04120.2447-26.9659-19.806-1.4227
95.1304-1.2933-3.30268.2252-5.52558.15150.04460.0771-0.02390.0094-0.21250.4215-0.34410.09140.20410.2188-0.0273-0.0140.2615-0.02550.184-13.05258.108-16.0968
105.96972.22190.39954.1866-0.02750.9133-0.3103-0.6103-0.58510.5864-0.0363-0.34550.96660.01740.24470.39850.05740.05750.23660.03970.2048-14.0108-3.8996-4.1142
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 31 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 54 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 55 through 81 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 82 through 160 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 161 through 252 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 253 through 297 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 298 through 316 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 317 through 350 )A0
9X-RAY DIFFRACTION9chain 'I' and (resid 5 through 11 )I0
10X-RAY DIFFRACTION10chain 'I' and (resid 12 through 24 )I0

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