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- PDB-5l0n: PKG I's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B... -

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Basic information

Entry
Database: PDB / ID: 5l0n
TitlePKG I's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with RP-cGMP
ComponentscGMP-dependent protein kinase 1
Keywordstransferase/transferase inhibitor / Binding Sites / Cyclic AMP / Cyclic GMP / Cyclic GMP-Dependent Protein Kinase Type I / Mutagenesis / Site-Directed / Protein Binding / analogs / transferase / transferase-transferase inhibitor complex
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
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. ...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 / Jelly Rolls / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / Jelly Rolls / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-6ZA / cGMP-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.285 Å
AuthorsCampbell, J.C. / Sankaran, B. / Kim, C.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM090161-02 United States
CitationJournal: To Be Published
Title: Structure of PKG I CNB-B bound to RP-cGMP
Authors: Campbell, J.C. / Sankaran, B. / Kim, C.W.
History
DepositionJul 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,6707
Polymers14,9871
Non-polymers6846
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.889, 54.305, 56.450
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 , 1 types, 1 molecules A

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


Mass: 14986.738 Da / Num. of mol.: 1 / Fragment: unp residues 219-351
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, cGMP-dependent protein kinase

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Non-polymers , 5 types, 147 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-6ZA / 2-amino-9-[(2R,4aR,6R,7R,7aS)-2,7-dihydroxy-2-sulfanylidenetetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]-3,9-dihydro-6H-purin-6-one


Mass: 361.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O6PS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.8 M Lithium sulfate monohydrate. 0.1 M Sodium acetate trihydrate pH 4.0, 4% v/v Polyethylene glycol 200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.28→39.88 Å / Num. obs: 31866 / % possible obs: 99.8 % / Redundancy: 8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.4
Reflection shellResolution: 1.29→1.31 Å / Redundancy: 7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.9 / CC1/2: 0.915 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ku8

4ku8


Resolution: 1.285→32.577 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.42
RfactorNum. reflection% reflection
Rfree0.1821 1572 4.94 %
Rwork0.1671 --
obs0.1678 31845 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.285→32.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms967 0 41 141 1149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081051
X-RAY DIFFRACTIONf_angle_d0.9661427
X-RAY DIFFRACTIONf_dihedral_angle_d12.289373
X-RAY DIFFRACTIONf_chiral_restr0.084160
X-RAY DIFFRACTIONf_plane_restr0.006182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2852-1.32660.23331450.24132690X-RAY DIFFRACTION100
1.3266-1.37410.26691660.222685X-RAY DIFFRACTION100
1.3741-1.42910.261510.20372702X-RAY DIFFRACTION100
1.4291-1.49410.20751370.19982709X-RAY DIFFRACTION100
1.4941-1.57290.19331400.18242740X-RAY DIFFRACTION100
1.5729-1.67140.16891200.16622739X-RAY DIFFRACTION100
1.6714-1.80050.19671280.16952756X-RAY DIFFRACTION100
1.8005-1.98160.18541230.16332782X-RAY DIFFRACTION100
1.9816-2.26830.17811500.15032766X-RAY DIFFRACTION100
2.2683-2.85760.16721560.1562807X-RAY DIFFRACTION100
2.8576-32.58730.16491560.16032897X-RAY DIFFRACTION99
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)
16.6738-1.15234.57125.8451-5.91132.00030.02310.6716-0.0752-0.78310.03760.08260.3109-0.0797-0.06060.19430.0105-0.0020.1752-0.01980.108-8.273851.89482.8674
24.25722.87590.3282.33650.37510.1503-0.10360.23820.2207-0.11630.0530.1581-0.058-0.06040.05170.09560.0214-0.00980.1010.00420.0951-2.584859.250211.0705
37.49613.01754.18685.08923.88952.00120.1321-0.48180.23710.2650.0688-0.3979-0.32830.1746-0.19920.1519-0.0015-0.00870.1359-0.0230.162915.594563.913319.2667
43.24290.85250.4941.13560.08470.7515-0.0059-0.0455-0.00320.031-0.02580.18610.0211-0.11630.03090.08320.00250.00480.0753-0.01590.10291.10560.054914.8075
522229.29587.2670.6781-2.46460.02020.8233-0.52480.21130.4862-0.2315-0.15380.27550.00830.07050.38740.09760.31-20.342353.953222.5679
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 220 through 232 )
2X-RAY DIFFRACTION2chain 'A' and (resid 233 through 278 )
3X-RAY DIFFRACTION3chain 'A' and (resid 279 through 293 )
4X-RAY DIFFRACTION4chain 'A' and (resid 294 through 340 )
5X-RAY DIFFRACTION5chain 'A' and (resid 341 through 346 )

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