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- PDB-4r4l: Crystal structure of wt cGMP dependent protein kinase I alpha (PK... -

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Basic information

Entry
Database: PDB / ID: 4r4l
TitleCrystal structure of wt cGMP dependent protein kinase I alpha (PKGI alpha) leucine zipper
ComponentscGMP-dependent protein kinase 1
KeywordsDNA BINDING PROTEIN / Leucine Zipper / Kinase / Binding Domain / MYPT1 / RhoA
Function / homology
Function and homology information


negative regulation of inositol phosphate biosynthetic process / negative regulation of glutamate secretion / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / cell growth involved in cardiac muscle cell development / regulation of testosterone biosynthetic process / collateral sprouting / negative regulation of vascular associated smooth muscle cell migration / negative regulation of platelet aggregation / relaxation of vascular associated smooth muscle ...negative regulation of inositol phosphate biosynthetic process / negative regulation of glutamate secretion / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / cell growth involved in cardiac muscle cell development / regulation of testosterone biosynthetic process / collateral sprouting / negative regulation of vascular associated smooth muscle cell migration / negative regulation of platelet aggregation / relaxation of vascular associated smooth muscle / positive regulation of circadian rhythm / Rap1 signalling / mitogen-activated protein kinase p38 binding / regulation of GTPase activity / cGMP-mediated signaling / dendrite development / spermatid development / cGMP effects / negative regulation of vascular associated smooth muscle cell proliferation / calcium channel regulator activity / cGMP binding / forebrain development / cerebellum development / acrosomal vesicle / neuron migration / sarcolemma / Ca2+ pathway / positive regulation of cytosolic calcium ion concentration / actin cytoskeleton organization / protein kinase activity / protein phosphorylation / protein serine kinase activity / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Single helix bin / cGMP-dependent protein kinase, N-terminal coiled-coil domain / Coiled-coil N-terminus of cGMP-dependent protein kinase / cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / 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 ...Single helix bin / cGMP-dependent protein kinase, N-terminal coiled-coil domain / Coiled-coil N-terminus of cGMP-dependent protein kinase / cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / 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 / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
HEXANE-1,6-DIOL / cGMP-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.245 Å
AuthorsReger, A.S. / Guo, E. / Yang, M.P. / Qin, L. / Kim, C.
CitationJournal: Biochemistry / Year: 2015
Title: Structures of cGMP-Dependent Protein Kinase (PKG) I alpha Leucine Zippers Reveal an Interchain Disulfide Bond Important for Dimer Stability.
Authors: Qin, L. / Reger, A.S. / Guo, E. / Yang, M.P. / Zwart, P. / Casteel, D.E. / Kim, C.
History
DepositionAug 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cGMP-dependent protein kinase 1
B: cGMP-dependent protein kinase 1
C: cGMP-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9756
Polymers17,6423
Non-polymers3323
Water46826
1
A: cGMP-dependent protein kinase 1
B: cGMP-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0945
Polymers11,7622
Non-polymers3323
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-24 kcal/mol
Surface area6800 Å2
MethodPISA
2
C: cGMP-dependent protein kinase 1

C: cGMP-dependent protein kinase 1


Theoretical massNumber of molelcules
Total (without water)11,7622
Polymers11,7622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area2750 Å2
ΔGint-25 kcal/mol
Surface area6890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.926, 95.926, 63.805
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11B-101-

SO4

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Components

#1: Protein/peptide cGMP-dependent protein kinase 1 / cGK 1 / cGK1 / cGMP-dependent protein kinase I / cGKI


Mass: 5880.826 Da / Num. of mol.: 3 / Fragment: alpha leucine zipper, UNP residues 2-48
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKG1, PRKG1B, PRKGR1A, PRKGR1B / Production host: Escherichia coli (E. coli) / References: UniProt: Q13976
#2: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL / 1,6-Hexanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 40% PEG 400, 200 mM Lithium Sulfate, 0.1 M Tris base/ Hydrochloric acid, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977488 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 19, 2012
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977488 Å / Relative weight: 1
ReflectionResolution: 2.245→15 Å / Num. all: 8669 / Num. obs: 8669 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.245→14.921 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 29.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2898 866 10.02 %Random
Rwork0.254 ---
all0.2576 8669 --
obs0.2576 8646 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.245→14.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1098 0 17 26 1141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021118
X-RAY DIFFRACTIONf_angle_d0.5011486
X-RAY DIFFRACTIONf_dihedral_angle_d12.984446
X-RAY DIFFRACTIONf_chiral_restr0.031176
X-RAY DIFFRACTIONf_plane_restr0.001192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2448-2.38490.31881410.28271251X-RAY DIFFRACTION99
2.3849-2.56820.31381410.26861267X-RAY DIFFRACTION100
2.5682-2.82510.2971410.27481274X-RAY DIFFRACTION100
2.8251-3.23030.2941410.27571285X-RAY DIFFRACTION100
3.2303-4.05620.26351460.25421312X-RAY DIFFRACTION100
4.0562-14.92090.29411560.23411391X-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)
11.3637-0.2679-0.31754.57115.39176.11690.0252-0.14680.25560.24870.2467-0.90050.16220.2581-0.19180.29360.03730.0020.3855-0.02360.422217.851930.13074.7808
23.38823.01831.30175.78413.9112.9460.0446-0.1250.6393-0.3282-0.19460.2758-0.0901-0.00450.23010.26690.03390.01230.3328-0.02750.369713.462832.3789-0.3606
31.3757-1.8701-0.81143.18010.60790.4306-0.6019-0.20.7820.68440.5565-0.3728-0.7340.494-0.03740.9399-0.0624-0.35350.3857-0.04030.86331.385737.42423.1957
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 47 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 47 )
3X-RAY DIFFRACTION3chain 'C' and (resid -1 through 47 )

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