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- PDB-5nw8: Crystal Structure of the Protein-Kinase A catalytic subunit from ... -

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Basic information

Entry
Database: PDB / ID: 5nw8
TitleCrystal Structure of the Protein-Kinase A catalytic subunit from Criteculus Griseus in complex with compounds RKp032 and Fasudil
Components
  • UPF0418 protein FAM164A
  • cAMP-dependent protein kinase catalytic subunit alphaCAMP-dependent pathway
KeywordsTRANSFERASE / Complex / peptidic ligand / ribose
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 / 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
5-(1,4-DIAZEPAN-1-SULFONYL)ISOQUINOLINE / 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: 2.086 Å
AuthorsMueller, J.M. / Heine, A. / Klebe, G.
Funding support1items
OrganizationGrant numberCountry
Loewe Corporation
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
DepositionMay 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation / citation_author / 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
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.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _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
D: UPF0418 protein FAM164A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4615
Polymers42,9022
Non-polymers5603
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-16 kcal/mol
Surface area15660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.515, 73.112, 77.317
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 / CAMP-dependent pathway / PKA C-alpha


Mass: 40998.551 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: 1903.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PKI 5-22 with S14RBS mutation / Source: (synth.) Cricetulus griseus (Chinese hamster) / References: UniProt: G3HK48
#5: 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

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Non-polymers , 3 types, 182 molecules

#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-M77 / 5-(1,4-DIAZEPAN-1-SULFONYL)ISOQUINOLINE / Fasudil / (5-ISOQUINOLINESULFONYL)HOMOPIPERAZINE / Fasudil


Mass: 291.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17N3O2S / Comment: inhibitor*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 5 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 Fasudil x HCl, 16 % 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: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.086→42.209 Å / Num. obs: 23612 / % possible obs: 98 % / Redundancy: 5.2 % / CC1/2: 0.997 / Rsym value: 0.075 / Net I/σ(I): 16.9
Reflection shellResolution: 2.09→2.21 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 4.95 / Num. unique obs: 3709 / CC1/2: 0.91 / Rsym value: 0.375 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
PHASERphasing
Cootmodel building
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.086→42.209 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2118 1181 5 %Random selection
Rwork0.1767 ---
obs0.1784 23610 98.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.086→42.209 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2845 0 31 180 3056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072974
X-RAY DIFFRACTIONf_angle_d0.7954045
X-RAY DIFFRACTIONf_dihedral_angle_d16.1371744
X-RAY DIFFRACTIONf_chiral_restr0.051434
X-RAY DIFFRACTIONf_plane_restr0.005533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0859-2.18080.27711420.2342702X-RAY DIFFRACTION97
2.1808-2.29580.24211470.19062787X-RAY DIFFRACTION99
2.2958-2.43960.21781410.18352685X-RAY DIFFRACTION95
2.4396-2.6280.24631480.18982809X-RAY DIFFRACTION100
2.628-2.89240.24891510.19152867X-RAY DIFFRACTION100
2.8924-3.31080.22041490.18682825X-RAY DIFFRACTION99
3.3108-4.17060.17151470.15962800X-RAY DIFFRACTION97
4.1706-42.21740.18471560.15392954X-RAY DIFFRACTION98
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)
10.0496-0.1284-0.17210.33230.44680.60060.0332-0.16890.17630.01150.1348-0.0942-0.13740.31410.20960.2051-0.0989-0.06090.3280.05830.20525.02230.584716.7818
20.4379-0.44750.13270.6914-0.13330.04030.00520.2805-0.0647-0.2720.04640.1988-0.130.0360.04790.228-0.01950.05450.21490.00610.182711.779315.6455-3.8041
30.14890.1859-0.09520.4336-0.23910.2916-0.14210.0593-0.0615-0.25950.03960.0522-0.03040.009-0.08730.1008-0.001-0.01550.2179-0.03810.20519.423814.0181-2.3783
40.4867-0.0252-0.10070.38780.08660.379-0.06950.045-0.0783-0.01-0.0006-0.0101-0.01090.1803-0.01580.10850.0081-0.00070.1379-0.00020.110312.120916.414612.7648
50.78590.0789-0.25760.8027-0.43540.59290.0207-0.2380.10620.1722-0.01290.2047-0.08640.1121-0.05950.14940.0170.02550.0924-0.02720.11795.646219.241527.2968
60.36470.058-0.40560.43210.28290.7146-0.04750.0099-0.1583-0.1060.04180.1140.04050.0555-0.00050.1015-0.0305-0.01830.1060.04020.168712.271312.7987.12
70.0040.01960.01670.09760.08130.0675-0.067-0.1293-0.2102-0.0445-0.01160.1375-0.13320.0123-0.00280.1575-0.0170.06510.1660.03190.3052-6.41712.399329.6877
80.00020.00120.00160.00340.0050.007-0.07870.0115-0.2247-0.1463-0.11940.2173-0.2458-0.0724-0.01370.17770.0008-0.06290.0747-0.00030.2917-4.833111.374918.7124
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 297 )
6X-RAY DIFFRACTION6chain 'A' and (resid 298 through 350 )
7X-RAY DIFFRACTION7chain 'D' and (resid 11 through 18 )
8X-RAY DIFFRACTION8chain 'D' and (resid 19 through 28 )

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