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- PDB-5kjy: Co-crystal structure of PKA RI alpha CNB-B mutant (G316R/A336T) w... -

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Basic information

Entry
Database: PDB / ID: 5kjy
TitleCo-crystal structure of PKA RI alpha CNB-B mutant (G316R/A336T) with cAMP
ComponentscAMP-dependent protein kinase type I-alpha regulatory subunit
KeywordsSIGNALING PROTEIN / Cyclic nucleotide / cAMP-dependent protein kinase / nucleotide selectivity / cyclic nucleotide binding domain
Function / homology
Function and homology information


cAMP-dependent protein kinase regulator activity / sperm head-tail coupling apparatus / nucleotide-activated protein kinase complex / ALK mutants bind TKIs / negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cardiac muscle cell proliferation / sarcomere organization / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation ...cAMP-dependent protein kinase regulator activity / sperm head-tail coupling apparatus / nucleotide-activated protein kinase complex / ALK mutants bind TKIs / negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cardiac muscle cell proliferation / sarcomere organization / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / cAMP-dependent protein kinase complex / ciliary base / protein kinase A catalytic subunit binding / negative regulation of activated T cell proliferation / mesoderm formation / PKA activation in glucagon signalling / plasma membrane raft / DARPP-32 events / Hedgehog 'off' state / cAMP binding / multivesicular body / cellular response to glucagon stimulus / FCGR3A-mediated IL10 synthesis / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / Signaling by ALK fusions and activated point mutants / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / intracellular signal transduction / protein domain specific binding / negative regulation of gene expression / centrosome / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / glutamatergic synapse / protein-containing complex / membrane / cytosol / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain ...cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / cAMP-dependent protein kinase type I-alpha regulatory subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLorenz, R. / Moon, E. / Kim, J.J. / Huang, G.Y. / Kim, C. / Herberg, F.W.
Funding support Germany, United States, 3items
OrganizationGrant numberCountry
Federal Ministry of Education and Research GrantFKZ 0316177F (No Pain) Germany
The Center for Interdisciplinary Nanostructure Science and Technology (CINSaT) of the University of Kassel Germany
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R01GM090161-06 United States
CitationJournal: Biochem. J. / Year: 2017
Title: Mutations of PKA cyclic nucleotide-binding domains reveal novel aspects of cyclic nucleotide selectivity.
Authors: Lorenz, R. / Moon, E.W. / Kim, J.J. / Schmidt, S.H. / Sankaran, B. / Pavlidis, I.V. / Kim, C. / Herberg, F.W.
History
DepositionJun 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Aug 2, 2017Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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 type I-alpha regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4162
Polymers17,0871
Non-polymers3291
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.700, 98.700, 36.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Detailsmonomer according to gel filtration

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Components

#1: Protein cAMP-dependent protein kinase type I-alpha regulatory subunit / Tissue-specific extinguisher 1 / TSE1


Mass: 17086.668 Da / Num. of mol.: 1 / Mutation: G316R, A336T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAR1A, PKR1, PRKAR1, TSE1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P10644
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.98 Å3/Da / Density % sol: 58.68 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 2.5M NaCl, 0.1M sodium acetate/acetic acid pH 4.7, 0.2M lithium sulfate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 5, 2012
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2→33.31 Å / Num. obs: 13793 / % possible obs: 99.6 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 5 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 3.1 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RGS

1rgs


Resolution: 2→32.307 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.71
RfactorNum. reflection% reflection
Rfree0.2214 684 4.96 %
Rwork0.1746 --
obs0.177 13791 99.5 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Bsol: 53.095 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7765 Å2-0 Å2-0 Å2
2--1.7765 Å20 Å2
3----3.5531 Å2
Refinement stepCycle: LAST / Resolution: 2→32.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1105 0 22 82 1209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071159
X-RAY DIFFRACTIONf_angle_d1.0821572
X-RAY DIFFRACTIONf_dihedral_angle_d15.855446
X-RAY DIFFRACTIONf_chiral_restr0.069179
X-RAY DIFFRACTIONf_plane_restr0.005200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.15450.26991370.21212593X-RAY DIFFRACTION100
2.1545-2.37130.25591350.20422608X-RAY DIFFRACTION100
2.3713-2.71420.25241350.1882624X-RAY DIFFRACTION100
2.7142-3.41910.23111370.16662629X-RAY DIFFRACTION100
3.4191-32.31130.1931400.16012653X-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)
18.9558-2.0381-5.34117.21524.29054.76960.3570.8515-0.4423-0.8657-0.4216-0.55870.39840.07440.18620.47380.16040.02790.2970.02090.346150.9719-23.3582.5897
23.42290.80223.67889.0080.65613.9948-0.1865-0.859-0.91620.19280.00280.66071.3128-0.69490.10580.3173-0.01230.05070.21030.00730.283339.7806-20.855111.0432
34.96183.72482.75214.5134.10033.9348-0.06460.0998-0.2473-0.58850.0807-0.16740.3331-0.1967-0.00020.38650.0023-0.06920.1991-0.01090.262242.7133-22.40980.2186
46.8386-3.08350.60984.9132-0.48613.8842-0.01330.38070.9049-0.1514-0.3163-0.3819-0.93990.45110.2070.3598-0.0044-0.05150.16470.06060.247548.60370.44165.7818
54.7566-1.8249-1.14925.68630.17451.1635-0.0850.27610.1997-0.5395-0.01180.0585-0.42850.32270.0390.3121-0.0244-0.0580.09010.02520.120945.9606-7.56877.8993
63.1891-1.4269-0.08732.41650.77723.2713-0.3126-0.01520.81230.0683-0.05980.1951-0.642-0.42610.23480.35620.091-0.05290.2791-0.03280.31839.65785.705616.295
73.2179-0.983-0.47277.3411-0.47112.33180.2112-0.0088-0.0105-0.3242-0.15740.5241-0.1538-0.3046-0.07420.30720.0188-0.02240.1854-0.04210.188739.9567-4.69228.7851
89.19472.9891.87915.98451.25314.4502-0.08070.48160.0435-0.9017-0.02780.3365-0.2588-0.17580.13720.39110.0415-0.03930.16760.0190.176744.3286-10.73130.7068
99.0407-5.2675-7.04289.53146.27269.653-0.19020.2961-0.4338-0.3148-0.01291.10320.4333-0.69580.10960.2832-0.0657-0.10110.3073-0.00440.412131.7913-15.20394.9269
102.0961-0.25920.23963.60475.37658.2894-0.3512-0.99380.4180.9689-0.03351.3740.0503-1.51220.37040.39150.10080.12030.4852-0.05880.494432.0374-2.78916.1855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 236:250)
2X-RAY DIFFRACTION2chain 'A' and (resseq 251:258)
3X-RAY DIFFRACTION3chain 'A' and (resseq 259:274)
4X-RAY DIFFRACTION4chain 'A' and (resseq 275:288)
5X-RAY DIFFRACTION5chain 'A' and (resseq 289:303)
6X-RAY DIFFRACTION6chain 'A' and (resseq 304:316)
7X-RAY DIFFRACTION7chain 'A' and (resseq 317:342)
8X-RAY DIFFRACTION8chain 'A' and (resseq 343:356)
9X-RAY DIFFRACTION9chain 'A' and (resseq 357:370)
10X-RAY DIFFRACTION10chain 'A' and (resseq 371:377)

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