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- PDB-6i2h: Crystal Structure of the Protein-Kinase A catalytic subunit from ... -

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Basic information

Entry
Database: PDB / ID: 6i2h
TitleCrystal Structure of the Protein-Kinase A catalytic subunit from Cricetulus Griseus in complex with compounds RKp182 and RKp190
Components
  • UPF0418 protein FAM164A
  • cAMP-dependent protein kinase catalytic subunit alpha
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 / cellular response to cold / cAMP-dependent protein kinase / regulation of osteoblast differentiation / cAMP-dependent protein kinase activity / sperm capacitation ...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 / cellular response to cold / cAMP-dependent protein kinase / regulation of osteoblast differentiation / cAMP-dependent protein kinase activity / sperm capacitation / 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 / protein kinase A regulatory subunit binding / plasma membrane raft / axoneme / 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 / cellular response to glucagon stimulus / protein serine/threonine/tyrosine kinase activity / protein kinase A signaling / protein export from nucleus / acrosomal vesicle / positive regulation of protein export from nucleus / neural tube closure / cellular response to glucose stimulus / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / manganese ion binding / cellular response to heat / dendritic spine / regulation of cell cycle / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / 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
Chem-AO8 / 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: 1.68 Å
AuthorsMueller, J.M. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other government Germany
CitationJournal: To be published
Title: Crystal Structure of the Protein-Kinase A catalytic subunit from Cricetulus Griseus in complex with compounds RKp182 and RKp190
Authors: Mueller, J.M. / Kirschner, R. / Heine, A. / Geyer, A. / Klebe, G.
History
DepositionNov 1, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionNov 20, 2019ID: 6EME
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 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
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
D: UPF0418 protein FAM164A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7695
Polymers43,1982
Non-polymers5713
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-8 kcal/mol
Surface area16650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.470, 71.698, 109.612
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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Protein / Protein/peptide / Sugars , 3 types, 3 molecules AD

#1: Protein cAMP-dependent protein kinase catalytic subunit alpha / 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 UPF0418 protein FAM164A


Mass: 2004.188 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: PKI 5-22 with G17RBS mutation. A ribose has been covalently attached to a serine of the peptide
Source: (synth.) Cricetulus griseus (Chinese hamster) / References: UniProt: G3HK48
#4: Sugar ChemComp-RIP / beta-D-ribopyranose / beta-D-ribose / D-ribose / ribose / RIBOSE(PYRANOSE FORM)


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

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Non-polymers , 3 types, 198 molecules

#3: Chemical ChemComp-AO8 / [2-[[2-(isoquinolin-5-ylsulfonylamino)ethylamino]methyl]phenyl]boronic acid


Mass: 385.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20BN3O4S
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.07 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 100 mM Mes-Bis-Tris, 75 mM lithium chloride, 1 mM DTT, 0.1 mM sodium EDTA, 0.25 mM Mega 8, 0.7 mM peptidic ligand, 5 mM RKp190, 20% v/v methanol/water in reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.88559 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88559 Å / Relative weight: 1
ReflectionResolution: 1.68→45.313 Å / Num. obs: 53307 / % possible obs: 99.9 % / Redundancy: 7.39 % / CC1/2: 0.999 / Rsym value: 0.066 / Net I/σ(I): 15.16
Reflection shellResolution: 1.68→1.78 Å / Redundancy: 7.28 % / Mean I/σ(I) obs: 3.05 / Num. unique obs: 8418 / CC1/2: 0.898 / Rsym value: 0.498 / % possible all: 99.2

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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: 1.68→45.313 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.24
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 2666 5 %Random selection
Rwork0.181 ---
obs0.182 53303 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.68→45.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2900 0 34 196 3130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093038
X-RAY DIFFRACTIONf_angle_d1.024130
X-RAY DIFFRACTIONf_dihedral_angle_d13.7411786
X-RAY DIFFRACTIONf_chiral_restr0.056440
X-RAY DIFFRACTIONf_plane_restr0.007548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6786-1.70910.24411350.21592555X-RAY DIFFRACTION98
1.7091-1.7420.21761380.20292619X-RAY DIFFRACTION100
1.742-1.77750.22721390.1952641X-RAY DIFFRACTION100
1.7775-1.81620.22521370.2022617X-RAY DIFFRACTION100
1.8162-1.85840.26211400.21342653X-RAY DIFFRACTION100
1.8584-1.90490.2411380.19652626X-RAY DIFFRACTION100
1.9049-1.95640.20641400.1922664X-RAY DIFFRACTION100
1.9564-2.0140.21791390.18932627X-RAY DIFFRACTION100
2.014-2.0790.20631390.1862652X-RAY DIFFRACTION100
2.079-2.15330.20291390.18552643X-RAY DIFFRACTION100
2.1533-2.23950.1951400.17732655X-RAY DIFFRACTION100
2.2395-2.34140.17411400.17312664X-RAY DIFFRACTION100
2.3414-2.46480.17231400.17052659X-RAY DIFFRACTION100
2.4648-2.61930.1951410.17362667X-RAY DIFFRACTION100
2.6193-2.82150.2291410.18262679X-RAY DIFFRACTION100
2.8215-3.10530.22981420.19042703X-RAY DIFFRACTION100
3.1053-3.55450.20821420.1862701X-RAY DIFFRACTION100
3.5545-4.47770.17091450.16132748X-RAY DIFFRACTION100
4.4777-45.32920.19781510.18142864X-RAY DIFFRACTION100
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)
10.2532-0.19450.140.28830.0750.2995-0.0192-0.05180.09080.12110.00540.152-0.2281-0.12370.00040.2615-0.0845-0.04470.30290.03390.23999.3765-8.6186-0.5418
20.29470.1325-0.14661.24280.04760.19470.07650.0691-0.0375-0.2462-0.0755-0.32950.14210.2871-00.25580.03960.02470.36860.05450.344321.6081-15.2324-28.6439
30.89250.1628-0.18181.1246-0.00910.3990.01580.0320.003-0.0223-0.0675-0.02160.03340.0901-0.00020.18940.0104-0.00370.17970.0120.16612.9003-18.0139-19.0527
40.01970.01550.00280.01910.00240.0173-0.05430.1103-0.2019-0.1361-0.0370.18870.14220.0308-00.29330.0361-0.02440.2749-0.08850.3191-11.9446-30.5908-28.6609
50.099-0.26950.01350.89560.00680.07440.18630.3731-0.0227-0.3751-0.1442-0.2540.04130.0535-0.00870.34540.03170.0320.2711-0.01080.1717-1.3644-21.9522-32.1114
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 114 )
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 350 )
4X-RAY DIFFRACTION4chain 'D' and (resid 8 through 15 )
5X-RAY DIFFRACTION5chain 'D' and (resid 16 through 25 )

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