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- PDB-4ku8: Structures of PKGI Reveal a cGMP-Selective Activation Mechanism -

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Basic information

Entry
Database: PDB / ID: 4ku8
TitleStructures of PKGI Reveal a cGMP-Selective Activation Mechanism
ComponentscGMP-dependent Protein Kinase 1
KeywordsSIGNALING PROTEIN / cyclic nucleotide binding domain / cGMP
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 / cGMP-mediated signaling / mitogen-activated protein kinase p38 binding / regulation of GTPase activity / 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
GLYCINE / cGMP-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.994 Å
AuthorsHuang, G.Y. / Kim, J.J. / Reger, A.S. / Lorenz, R. / Moon, E.W. / Casteel, D.E. / Sankaran, B. / Herberg, F.W. / Kim, C.
CitationJournal: Structure / Year: 2014
Title: Structural Basis for Cyclic-Nucleotide Selectivity and cGMP-Selective Activation of PKG I.
Authors: Huang, G.Y. / Kim, J.J. / Reger, A.S. / Lorenz, R. / Moon, E.W. / Zhao, C. / Casteel, D.E. / Bertinetti, D. / Vanschouwen, B. / Selvaratnam, R. / Pflugrath, J.W. / Sankaran, B. / Melacini, G. ...Authors: Huang, G.Y. / Kim, J.J. / Reger, A.S. / Lorenz, R. / Moon, E.W. / Zhao, C. / Casteel, D.E. / Bertinetti, D. / Vanschouwen, B. / Selvaratnam, R. / Pflugrath, J.W. / Sankaran, B. / Melacini, G. / Herberg, F.W. / Kim, C.
History
DepositionMay 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: cGMP-dependent Protein Kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0636
Polymers50,8373
Non-polymers2253
Water6,197344
1
A: cGMP-dependent Protein Kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0963
Polymers16,9461
Non-polymers1502
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)17,0212
Polymers16,9461
Non-polymers751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: cGMP-dependent Protein Kinase 1


Theoretical massNumber of molelcules
Total (without water)16,9461
Polymers16,9461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.766, 78.766, 147.001
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 16945.816 Da / Num. of mol.: 3
Fragment: Carboxyl Cyclic Nucleotide Binding Domain, UNP residues 204-354
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKG1, PRKG1B, PRKGR1A, PRKGR1B / Plasmid: pQTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13976
#2: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5.5
Details: 0.1M SPG buffer, 25% PEG1500, pH 5.5, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 20, 2010
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.994→36.9 Å / Num. all: 36736 / Num. obs: 36516 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.994→2.0476 Å / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.7.2_869)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.994→34.107 Å / SU ML: 0.51 / σ(F): 1.34 / Phase error: 24.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2447 1812 4.97 %5.0% of the observed intensities were excluded from refinement for cross validation purposes.
Rwork0.1974 ---
all0.2441 36781 --
obs0.1997 36450 99.14 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.177 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.4847 Å2-0 Å20 Å2
2--4.4847 Å20 Å2
3----8.9694 Å2
Refinement stepCycle: LAST / Resolution: 1.994→34.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2910 0 15 344 3269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063001
X-RAY DIFFRACTIONf_angle_d0.984066
X-RAY DIFFRACTIONf_dihedral_angle_d15.9691071
X-RAY DIFFRACTIONf_chiral_restr0.072465
X-RAY DIFFRACTIONf_plane_restr0.004531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.994-2.04760.27331270.23382449X-RAY DIFFRACTION93
2.0476-2.10780.28381430.22832659X-RAY DIFFRACTION100
2.1078-2.17580.28981370.21542632X-RAY DIFFRACTION100
2.1758-2.25360.26841390.22432670X-RAY DIFFRACTION100
2.2536-2.34380.25481340.21992629X-RAY DIFFRACTION100
2.3438-2.45040.28811410.21362682X-RAY DIFFRACTION100
2.4504-2.57960.29841360.21182640X-RAY DIFFRACTION100
2.5796-2.74110.2681410.20372676X-RAY DIFFRACTION100
2.7411-2.95270.23771350.19772671X-RAY DIFFRACTION100
2.9527-3.24960.2671460.20952708X-RAY DIFFRACTION100
3.2496-3.71930.22151430.19072706X-RAY DIFFRACTION100
3.7193-4.6840.21861420.15762729X-RAY DIFFRACTION100
4.684-34.11180.22281480.20352787X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.5654.53410.46536.98022.39815.12180.375-0.4435-0.40990.3175-0.5601-0.2912-0.26750.14040.08720.2977-0.0089-0.00170.19020.1320.2879-28.292936.5138-17.8799
22.3604-1.59461.90958.008-5.9194.63540.13060.1968-1.3502-1.4728-0.0014-0.14411.99370.5898-0.00340.72320.1130.05440.17040.01770.4134-32.76727.735-28.6915
32.1858-4.2291-0.15158.98111.05962.0490.17540.73560.5176-0.6258-0.2643-0.5831-0.34310.17470.09250.3219-0.01840.05930.24580.07150.2789-32.24937.8432-27.9983
49.56658.7162-6.67218.9443-6.19274.66930.90350.13780.54931.11230.04980.5749-1.1809-0.1454-1.07060.42420.06240.09110.26080.02690.3045-40.568936.1421-13.6677
52.50360.4055-0.33224.1454-0.8324.23780.21990.029-0.06010.1107-0.19350.242-0.1899-0.8504-0.10220.1572-0.0412-0.00250.25080.08810.1117-46.888824.8657-13.0621
60.5034-1.6366-0.86316.80681.01723.64620.56470.8736-0.4344-0.1356-0.52761.85610.9173-2.15430.01580.4452-0.2601-0.13410.96170.05540.4359-57.43899.7462-10.8451
75.28431.91590.22943.5085-0.32671.09740.13970.25990.1941-0.2467-0.09450.13850.1773-0.2717-0.03540.2721-0.0356-0.03830.24120.0550.1503-44.675821.8292-19.5273
81.6511.8973-1.08484.3277-4.527.7950.05680.04860.0598-0.00060.21090.1781-0.2723-0.5861-0.25930.23510.07120.0170.21330.03140.1987-42.871832.2113-21.6058
98.72185.8814-4.43764.1626-3.65384.5081-0.0944-0.5458-0.4550.0242-0.4208-0.08350.96890.54560.38790.560.11670.07470.3105-0.00660.1991-39.918720.7659-36.1277
102.43310.7302-0.5091.74272.213.9045-0.2283-0.79720.04051.0923-0.82661.56250.879-0.70540.35240.82960.11130.41730.7094-0.03150.7256-39.648454.6383-13.9533
112.78770.27390.78192.58040.05132.22910.29890.00391.16560.4201-0.20140.4208-1.08090.30920.00140.6128-0.08630.19150.06540.03820.4154-24.185856.7441-20.2795
126.3170.69340.91640.08480.09280.10310.3954-0.3946-0.25110.1633-0.1610.02420.0886-0.0316-0.1710.4512-0.0928-0.14220.20650.08310.2767-20.565823.6499-4.015
136.24190.1209-1.10951.9083-0.30292.58990.4159-0.6254-0.36050.0823-0.09210.16480.32790.1131-0.22370.5315-0.1781-0.19190.20330.04060.305-12.219926.53420.558
140.38060.5827-0.20010.9486-0.22670.1859-0.0542-0.1364-0.34410.0626-0.21460.027-0.0610.2505-0.17370.3834-0.1169-0.06310.55720.27551.2875-25.746234.4442-25.1473
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 217:232 )A217 - 232
2X-RAY DIFFRACTION2( CHAIN A AND RESID 233:241 )A233 - 241
3X-RAY DIFFRACTION3( CHAIN A AND RESID 242:249 )A242 - 249
4X-RAY DIFFRACTION4( CHAIN A AND RESID 250:257 )A250 - 257
5X-RAY DIFFRACTION5( CHAIN A AND RESID 258:285 )A258 - 285
6X-RAY DIFFRACTION6( CHAIN A AND RESID 286:293 )A286 - 293
7X-RAY DIFFRACTION7( CHAIN A AND RESID 294:318 )A294 - 318
8X-RAY DIFFRACTION8( CHAIN A AND RESID 319:344 )A319 - 344
9X-RAY DIFFRACTION9( CHAIN A AND RESID 345:366 )A345 - 366
10X-RAY DIFFRACTION10( CHAIN B AND RESID 225:257 )B225 - 257
11X-RAY DIFFRACTION11( CHAIN B AND RESID 258:338 )B258 - 338
12X-RAY DIFFRACTION12( CHAIN C AND RESID 217:278 )C217 - 278
13X-RAY DIFFRACTION13( CHAIN C AND RESID 279:344 )C279 - 344
14X-RAY DIFFRACTION14( CHAIN A AND RESID 401:402 ) OR ( CHAIN B AND RESID 401:401 )A401 - 402
15X-RAY DIFFRACTION14( CHAIN A AND RESID 401:402 ) OR ( CHAIN B AND RESID 401:401 )B401

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