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- PDB-7t4u: Crystal Structure of cGMP-dependent Protein Kinase -

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Basic information

Entry
Database: PDB / ID: 7t4u
TitleCrystal Structure of cGMP-dependent Protein Kinase
ComponentscGMP-dependent protein kinase 1
KeywordsTRANSFERASE / CYCLIC NUCLEOTIDE BINDING DOMAINS / CYCLIC NUCLEOTIDE PROTEIN KINASE / PKG / CGMP-DEPENDENT PROTEIN KINASE
Function / homology
Function and homology information


negative regulation of glutamate secretion / negative regulation of inositol phosphate biosynthetic process / 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 platelet aggregation / positive regulation of circadian rhythm / relaxation of vascular associated smooth muscle ...negative regulation of glutamate secretion / negative regulation of inositol phosphate biosynthetic process / 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 platelet aggregation / positive regulation of circadian rhythm / relaxation of vascular associated smooth muscle / Rap1 signalling / regulation of GTPase activity / cGMP-mediated signaling / mitogen-activated protein kinase p38 binding / negative regulation of vascular associated smooth muscle cell migration / cGMP effects / dendrite development / spermatid development / negative regulation of vascular associated smooth muscle cell proliferation / cGMP binding / forebrain development / calcium channel regulator activity / acrosomal vesicle / cerebellum development / sarcolemma / neuron migration / positive regulation of cytosolic calcium ion concentration / actin cytoskeleton organization / Ca2+ pathway / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Jelly Rolls / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-EX6 / cGMP-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.99 Å
AuthorsZebisch, M. / Silvestre, L. / Fischmann, T.O.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Commun Biol / Year: 2023
Title: Selective small molecule activation of PKG1alpha: structure and function
Authors: Metwally, E. / Mak, V. / Sylvestre, H.L. / McEwan, P. / Baker, J.J. / Rose, Y. / Patel, A. / Lim, Y.-H. / Healy, D. / Hanisak, J. / Ermakov, G. / Beaumont, M. / Cheng, A.C. / Greshock, T. / Fischmann, T.O.
History
DepositionDec 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_entry_details / pdbx_modification_feature
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)107,3854
Polymers106,3542
Non-polymers1,0312
Water5,531307
1
A: cGMP-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6932
Polymers53,1771
Non-polymers5151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: cGMP-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6932
Polymers53,1771
Non-polymers5151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.463, 102.709, 103.843
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 53177.102 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-EX6 / 3-amino-4-({(2S,3S)-3-[(1S)-1-(3,5-dichlorophenyl)-2-hydroxyethoxy]-2-phenylpiperidin-1-yl}methyl)benzoic acid


Mass: 515.428 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H28Cl2N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8 / Details: 0.1M MIB pH 9.0 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.99→73.024 Å / Num. obs: 45643 / % possible obs: 67.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 34.63 Å2 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.075 / Net I/σ(I): 8.8
Reflection shellResolution: 1.99→2.169 Å / Rmerge(I) obs: 1.278 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2283 / Rpim(I) all: 0.557

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
BUSTER2.11.7refinement
PDB_EXTRACT3.27data extraction
Aimlessdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.99→39.36 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.896 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.359 / SU Rfree Blow DPI: 0.242
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2244 4.92 %RANDOM
Rwork0.214 ---
obs0.216 45638 66.4 %-
Displacement parametersBiso max: 146.81 Å2 / Biso mean: 43.94 Å2 / Biso min: 13.85 Å2
Baniso -1Baniso -2Baniso -3
1-9.1154 Å20 Å20 Å2
2---5.2173 Å20 Å2
3----3.8981 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: final / Resolution: 1.99→39.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7424 0 377 0 7801
Biso mean--40.11 --
Num. residues----928
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3287SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2373HARMONIC5
X-RAY DIFFRACTIONt_it15052HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion987SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact15569SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d15052HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg27229HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.19
X-RAY DIFFRACTIONt_other_torsion17.11
LS refinement shellResolution: 1.99→2.09 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2913 49 5.37 %
Rwork0.2029 864 -
all0.2071 913 -
obs--9.82 %
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)
10.49450.5548-0.27030.6217-0.28690.1288-0.03160.0610.0105-0.1880.03450.1350.08030.0579-0.00290.14150.0167-0.0371-0.1216-0.0038-0.1692.22530.3608-7.0908
20.4009-0.3718-0.37740.51280.12550.3810.01460.081-0.0081-0.0659-0.06210.00780.0216-0.02130.04750.0851-0.0324-0.0269-0.1310.0116-0.153624.180820.914317.9737
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A220 - 9901
2X-RAY DIFFRACTION2{ B|* }B220 - 9901

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