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- PDB-6ema: Crystal Structure of the Protein-Kinase A catalytic subunit from ... -

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Basic information

Entry
Database: PDB / ID: 6ema
TitleCrystal Structure of the Protein-Kinase A catalytic subunit from Criteculus Griseus in complex with compounds RKp120 and ATP
Components
  • cAMP-dependent protein kinase catalytic subunit alphaCAMP-dependent pathway
  • cAMP-dependent protein kinase inhibitorCAMP-dependent pathway
KeywordsTRANSFERASE / Complex / peptidic ligand
Function / homology
Function and homology information


regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / sperm capacitation / regulation of osteoblast differentiation / cAMP-dependent protein kinase activity ...regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / sperm capacitation / regulation of osteoblast differentiation / cAMP-dependent protein kinase activity / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / axoneme / plasma membrane raft / mesoderm formation / sperm flagellum / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / positive regulation of gluconeogenesis / negative regulation of TORC1 signaling / protein export from nucleus / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / positive regulation of protein export from nucleus / neural tube closure / cellular response to glucose stimulus / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / mRNA processing / cellular response to heat / manganese ion binding / dendritic spine / regulation of cell cycle / nuclear speck / protein domain specific binding / phosphorylation / protein serine kinase activity / centrosome / protein serine/threonine kinase activity / glutamatergic synapse / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / magnesium ion binding / mitochondrion / ATP binding / nucleus / cytosol / cytoplasm
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 / beta-D-ribopyranose / cAMP-dependent protein kinase inhibitor alpha / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsMueller, J.M. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
Loewe Corporation Germany
CitationJournal: Acs Omega / Year: 2019
Title: Conceptional Design of Self-Assembling Bisubstrate-like Inhibitors of Protein Kinase A Resulting in a Boronic Acid Glutamate Linkage
Authors: Mueller, J.M. / Kirschner, R. / Geyer, A. / Klebe, G.
History
DepositionOct 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity.formula_weight
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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
C: cAMP-dependent protein kinase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7974
Polymers43,1402
Non-polymers6572
Water2,162120
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint1 kcal/mol
Surface area15160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.860, 73.433, 76.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 41193.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Tissue: Ovary / Gene: PRKACA / Organ: Ovary
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P25321, cAMP-dependent protein kinase
#2: Protein/peptide cAMP-dependent protein kinase inhibitor / CAMP-dependent pathway


Mass: 1946.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PKI 5-22 with N20RBS mutation / Source: (synth.) Cricetulus griseus (Chinese hamster) / References: UniProt: G3HK48*PLUS
#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: Sugar ChemComp-RIP / beta-D-ribopyranose / Ribose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DRibpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-ribopyranoseCOMMON NAMEGMML 1.0
b-D-RibpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.42 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 100 mM Mes-Bis-Tris, 55 mM lithium chloride, 10 mM magnesium chloride, 1 mM DTT, 0.1 mM sodium EDTA, 0.25 mM Mega 8, 0.7 mM peptidic ligand, 2 mM ATP, 17% v/v methanol/water in reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.88→38.47 Å / Num. obs: 32196 / % possible obs: 99.2 % / Redundancy: 5.89 % / CC1/2: 1 / Rsym value: 0.043 / Net I/σ(I): 26.64
Reflection shellResolution: 1.88→1.99 Å / Redundancy: 6.03 % / Mean I/σ(I) obs: 3.66 / Num. unique obs: 5108 / CC1/2: 0.891 / Rsym value: 0.495 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→38.47 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.39
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 1610 5 %Random selection
Rwork0.1822 ---
obs0.1837 32194 99.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.88→38.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2799 0 29 120 2948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072909
X-RAY DIFFRACTIONf_angle_d0.8163961
X-RAY DIFFRACTIONf_dihedral_angle_d13.91692
X-RAY DIFFRACTIONf_chiral_restr0.052431
X-RAY DIFFRACTIONf_plane_restr0.006507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8794-1.93470.24721320.23362520X-RAY DIFFRACTION99
1.9347-1.99710.24771320.21532496X-RAY DIFFRACTION100
1.9971-2.06850.27611320.19862516X-RAY DIFFRACTION99
2.0685-2.15130.2211330.20192522X-RAY DIFFRACTION99
2.1513-2.24920.2271320.18012502X-RAY DIFFRACTION99
2.2492-2.36780.20821330.17132543X-RAY DIFFRACTION100
2.3678-2.51610.22021350.1792547X-RAY DIFFRACTION100
2.5161-2.71030.19891330.18582539X-RAY DIFFRACTION99
2.7103-2.98290.25011330.19482532X-RAY DIFFRACTION99
2.9829-3.41440.24921360.19542579X-RAY DIFFRACTION100
3.4144-4.30080.19821370.16792593X-RAY DIFFRACTION99
4.3008-38.4780.17021420.16862695X-RAY DIFFRACTION99
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)
10.2105-0.23940.05680.86970.40650.386-0.0978-0.01790.2682-0.3693-0.1294-0.1353-0.20350.2638-0.06250.2558-0.0978-0.01490.32980.11350.249524.235630.691516.3695
20.5172-0.47620.24710.4401-0.2220.1162-0.13610.42980.0822-0.70880.23160.1093-0.2181-0.13220.00090.59840.03890.00680.5149-0.02080.347311.323915.8934-3.0712
30.65930.6047-0.53881.3923-1.05820.8304-0.20730.45320.0758-0.6784-0.04990.08820.011-0.1813-0.64260.28990.0056-0.10060.3361-0.06010.31068.896814.2352-2.0026
40.82010.2342-0.35741.06890.12710.8694-0.02820.1088-0.0902-0.1692-0.03820.06020.00540.1013-0.00010.18390.0183-0.01420.19730.00270.194112.158816.464912.9699
51.24290.16190.44511.3223-0.35230.81010.0163-0.05950.01720.0555-0.020.2744-0.0928-0.04670.00070.17950.03240.01270.1420.00280.2143.513219.656722.6461
60.54930.27410.13390.4394-0.11740.58570.0415-0.41750.06760.5764-0.0037-0.0091-0.22390.1060.0140.3193-0.02330.02620.2781-0.00610.17369.793618.621836.6534
70.4070.258-0.63851.02620.20561.3905-0.08170.0795-0.1413-0.1910.00030.15460.07950.0322-0.00040.1959-0.0152-0.01770.2263-0.02420.274212.555812.5118.1507
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 54 )
3X-RAY DIFFRACTION3chain 'A' and (resid 55 through 81 )
4X-RAY DIFFRACTION4chain 'A' and (resid 82 through 160 )
5X-RAY DIFFRACTION5chain 'A' and (resid 161 through 252 )
6X-RAY DIFFRACTION6chain 'A' and (resid 253 through 297 )
7X-RAY DIFFRACTION7chain 'A' and (resid 298 through 350 )

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