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- PDB-5h78: Crystal structure of the PKA-DHR14 fusion protein -

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Basic information

Entry
Database: PDB / ID: 5h78
TitleCrystal structure of the PKA-DHR14 fusion protein
ComponentscAMP-dependent protein kinase type II-alpha regulatory subunit,DHR14
KeywordsSIGNALING PROTEIN / DE NOVO PROTEIN / synthetic protein
Function / homology
Function and homology information


cAMP-dependent protein kinase regulator activity / ROBO receptors bind AKAP5 / nucleotide-activated protein kinase complex / negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase complex / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / ciliary base / protein kinase A catalytic subunit binding ...cAMP-dependent protein kinase regulator activity / ROBO receptors bind AKAP5 / nucleotide-activated protein kinase complex / negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase complex / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / ciliary base / protein kinase A catalytic subunit binding / plasma membrane raft / PKA activation in glucagon signalling / DARPP-32 events / cAMP binding / Hedgehog 'off' state / FCGR3A-mediated IL10 synthesis / 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 / 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 / focal adhesion / ubiquitin protein ligase binding / centrosome / protein-containing complex / extracellular exosome / membrane / plasma 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 / RmlC-like jelly roll fold
Similarity search - Domain/homology
cAMP-dependent protein kinase type II-alpha regulatory subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsYoun, S.J. / Kwon, N.Y. / Lee, J.H. / Kim, J.H. / Lee, H. / Lee, J.O.
CitationJournal: Sci Rep / Year: 2017
Title: Construction of novel repeat proteins with rigid and predictable structures using a shared helix method.
Authors: Youn, S.J. / Kwon, N.Y. / Lee, J.H. / Kim, J.H. / Choi, J. / Lee, H. / Lee, J.O.
History
DepositionNov 17, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 II-alpha regulatory subunit,DHR14
B: cAMP-dependent protein kinase type II-alpha regulatory subunit,DHR14


Theoretical massNumber of molelcules
Total (without water)44,6672
Polymers44,6672
Non-polymers00
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-18 kcal/mol
Surface area22170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.234, 96.539, 39.351
Angle α, β, γ (deg.)90.00, 89.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-205-

HOH

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Components

#1: Protein cAMP-dependent protein kinase type II-alpha regulatory subunit,DHR14


Mass: 22333.561 Da / Num. of mol.: 2 / Fragment: RESIDUES 4-40 (UNP RESIDUES 5-41),RESIDUES 41-196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others)
Gene: PRKAR2A, PKR2, PRKAR2 / Production host: Escherichia coli (E. coli) / References: UniProt: P13861
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 3.91 Å3/Da / Density % sol: 68.51 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 6.5
Details: 0.05M sodium cacodylate pH 6.5, 0.01M magnesium chloride, 0.2M potassium chloride, 12%(w/v) PEG 4000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 83181 / % possible obs: 98.7 % / Redundancy: 3.5 % / Net I/σ(I): 19.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 4.21 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IZX, 5CWH

2izx

5cwh


Resolution: 2.002→29.593 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.52
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2068 3689 4.43 %
Rwork0.181 --
obs0.1822 83181 93.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.002→29.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3060 0 0 445 3505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093080
X-RAY DIFFRACTIONf_angle_d0.8574156
X-RAY DIFFRACTIONf_dihedral_angle_d22.2551976
X-RAY DIFFRACTIONf_chiral_restr0.051520
X-RAY DIFFRACTIONf_plane_restr0.005528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0018-2.02820.24061310.24572687X-RAY DIFFRACTION83
2.0282-2.05590.2891110.23173057X-RAY DIFFRACTION90
2.0559-2.08530.27331470.21772994X-RAY DIFFRACTION92
2.0853-2.11640.19371020.21512987X-RAY DIFFRACTION92
2.1164-2.14950.22421310.19913018X-RAY DIFFRACTION92
2.1495-2.18470.22811460.18933127X-RAY DIFFRACTION92
2.1847-2.22240.1731640.17692937X-RAY DIFFRACTION93
2.2224-2.26280.19121320.18493020X-RAY DIFFRACTION93
2.2628-2.30630.17211070.18563099X-RAY DIFFRACTION92
2.3063-2.35330.25481570.18722977X-RAY DIFFRACTION94
2.3533-2.40450.21041310.18383081X-RAY DIFFRACTION94
2.4045-2.46040.20871720.17643078X-RAY DIFFRACTION93
2.4604-2.52190.23581370.17963044X-RAY DIFFRACTION95
2.5219-2.590.23171570.17613065X-RAY DIFFRACTION94
2.59-2.66620.22991460.16583083X-RAY DIFFRACTION95
2.6662-2.75220.18521370.17633119X-RAY DIFFRACTION95
2.7522-2.85050.15841560.17653051X-RAY DIFFRACTION95
2.8505-2.96450.23181350.16643174X-RAY DIFFRACTION96
2.9645-3.09930.2121820.18783104X-RAY DIFFRACTION96
3.0993-3.26250.19911340.18323128X-RAY DIFFRACTION96
3.2625-3.46660.18981520.16573170X-RAY DIFFRACTION96
3.4666-3.73380.19011270.15853123X-RAY DIFFRACTION96
3.7338-4.10870.18881500.16073131X-RAY DIFFRACTION96
4.1087-4.70120.18511370.15253171X-RAY DIFFRACTION96
4.7012-5.91520.22861550.19173189X-RAY DIFFRACTION98
5.9152-29.59590.21541530.23452878X-RAY DIFFRACTION88
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)
17.61412.62620.28627.0261-1.94797.34490.0753-0.39090.08360.5071-0.1986-0.2716-0.19450.16490.11260.14440.0464-0.00330.2755-0.050.2877-4.3718-52.42715.2097
23.9089-5.3472-4.31127.27725.88964.7476-0.2607-0.303-0.04210.41230.4677-0.33530.1710.3644-0.230.15460.0513-0.03850.296-0.0190.2482-17.4174-42.83819.9165
33.39460.28270.29331.32580.19111.8876-0.00560.0641-0.1015-0.01820.0252-0.09570.08820.1969-0.00530.14410.0280.00950.10980.0130.0619-37.0792-32.248619.2871
42.445-2.3784-1.79446.4654.72235.3594-0.0529-0.0767-0.2410.0983-0.08340.24510.3642-0.33040.07760.1572-0.05070.01560.16450.01650.1176-55.5472-36.811920.7794
53.76353.18271.57033.1781.35651.0155-0.06340.1070.0612-0.10540.119-0.19260.01620.1239-0.03760.14220.00010.02330.2121-0.00860.1559-19.0225-60.15730.656
62.8142-0.03450.11281.79710.75262.1096-0.03010.01360.1658-0.0046-0.0010.0745-0.2097-0.09750.030.1519-0.0142-0.00410.09690.02510.0575-47.9324-66.640.2823
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 57 )
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 157 )
4X-RAY DIFFRACTION4chain 'A' and (resid 158 through 196 )
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 97 )
6X-RAY DIFFRACTION6chain 'B' and (resid 98 through 196 )

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