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- PDB-7mbj: Crystal structure of cGMP dependent protein kinase I alpha (PKG I... -

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Basic information

Entry
Database: PDB / ID: 7mbj
TitleCrystal structure of cGMP dependent protein kinase I alpha (PKG I alpha)CNB-A domain with R177Q mutation
ComponentscGMP-dependent protein kinase 1
KeywordsSIGNALING PROTEIN / cGMP dependent protein kinase I alpha / second messenger / thoracic aortic aneurysms and aortic dissections causing mutation
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 / spermatid development / cGMP effects / negative regulation of vascular associated smooth muscle cell migration / dendrite development / negative regulation of vascular associated smooth muscle cell proliferation / cGMP binding / calcium channel regulator activity / 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 / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / 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
Similarity search - Domain/homology
cGMP-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsKim, J.J. / Casteel, D.E. / Kim, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM090161 United States
CitationJournal: Elife / Year: 2022
Title: An auto-inhibited state of protein kinase G and implications for selective activation.
Authors: Sharma, R. / Kim, J.J. / Qin, L. / Henning, P. / Akimoto, M. / VanSchouwen, B. / Kaur, G. / Sankaran, B. / MacKenzie, K.R. / Melacini, G. / Casteel, D.E. / Herberg, F.W. / Kim, C.W.
History
DepositionMar 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)30,5522
Polymers30,5522
Non-polymers00
Water6,503361
1
A: cGMP-dependent protein kinase 1


Theoretical massNumber of molelcules
Total (without water)15,2761
Polymers15,2761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cGMP-dependent protein kinase 1


Theoretical massNumber of molelcules
Total (without water)15,2761
Polymers15,2761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.198, 41.855, 48.312
Angle α, β, γ (deg.)94.739, 113.664, 114.027
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 15275.832 Da / Num. of mol.: 2 / Mutation: R177Q
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4.5 / Details: 6% Tacsimate (pH 4.5), 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.26→50 Å / Num. obs: 62350 / % possible obs: 93.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 14.06 Å2 / Rmerge(I) obs: 0.055 / Χ2: 1.071 / Net I/σ(I): 25.04
Reflection shellResolution: 1.26→1.31 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 6.56 / Num. unique obs: 5426 / Χ2: 1.064 / % possible all: 80.9

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3shr

3shr


Resolution: 1.26→36.54 Å / SU ML: 0.142 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 21.8058
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.197 3133 5.03 %
Rwork0.1775 59187 -
obs0.1785 62320 94.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.17 Å2
Refinement stepCycle: LAST / Resolution: 1.26→36.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1917 0 0 361 2278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092079
X-RAY DIFFRACTIONf_angle_d1.17752827
X-RAY DIFFRACTIONf_chiral_restr0.1086334
X-RAY DIFFRACTIONf_plane_restr0.0084357
X-RAY DIFFRACTIONf_dihedral_angle_d5.2366300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.280.28471470.2672394X-RAY DIFFRACTION85.79
1.28-1.30.25761380.24032662X-RAY DIFFRACTION92.32
1.3-1.330.24441140.22432614X-RAY DIFFRACTION92.29
1.33-1.350.24111420.21982674X-RAY DIFFRACTION92.75
1.35-1.380.27341430.20722636X-RAY DIFFRACTION93.35
1.38-1.40.25081460.20992661X-RAY DIFFRACTION93.26
1.4-1.430.22651430.2072666X-RAY DIFFRACTION93.76
1.43-1.470.24131340.19192694X-RAY DIFFRACTION94.14
1.47-1.50.20251430.18972711X-RAY DIFFRACTION94.13
1.5-1.540.19931500.18552647X-RAY DIFFRACTION94.27
1.54-1.590.22521360.18662717X-RAY DIFFRACTION95.1
1.59-1.640.20891410.18172737X-RAY DIFFRACTION95.2
1.64-1.70.19721460.18272729X-RAY DIFFRACTION95.32
1.7-1.770.18521490.18412716X-RAY DIFFRACTION95.92
1.77-1.850.20751370.17812749X-RAY DIFFRACTION95.94
1.85-1.950.22911490.17822747X-RAY DIFFRACTION96.44
1.95-2.070.18231540.17082747X-RAY DIFFRACTION96.89
2.07-2.230.17541400.16162786X-RAY DIFFRACTION97.5
2.23-2.450.191470.17142833X-RAY DIFFRACTION97.74
2.45-2.810.20971470.17872758X-RAY DIFFRACTION98.11
2.81-3.530.17591460.17272782X-RAY DIFFRACTION97.63
3.54-36.540.17971410.16262527X-RAY DIFFRACTION88.9
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)
15.15085279871.563863023620.4589900817275.29102062375-0.1126291093674.76252515649-0.0403888880102-0.303814967110.06577803759360.1742221288790.0339171221416-0.2032560891830.04551410296310.2403144915290.05188313277470.1425106556580.0697753400945-0.01563840606390.170314708281-0.05751187694660.103163431422-5.716664718532.0819229835215.8953247962
22.47661413811-0.5930159769551.520011101458.919497036246.795520383557.50342181772-0.1134218400460.006432811742530.233836086219-0.100851975292-0.1024280643220.162994118523-0.282125825452-0.1874794234110.2039594683070.107269308320.01500533491-0.003661564608750.07489694830650.01987585403040.0624262229697-9.81869182686-1.504387264582.9783521566
31.81510663792-0.5637608583732.492055482033.612163813250.1301321608624.899092235530.04246161719940.113536088945-0.44121948270.2419075073950.253175672418-0.2861816467980.775281231120.255040119191-0.3312422041020.2894841432520.0516809800987-0.02706750754150.151502743786-0.01861017029310.168936064077-4.98192622076-18.73659560632.50843093176
47.50771001238-8.42179384645-0.1634397027419.450758295220.1944679421372.071432314370.1878629566740.6905097803-0.0566405831367-0.2605846807230.0311828996497-0.9709393787770.4534156385760.974823238068-0.1724598624390.1708223980530.0622846341442-0.01151485924740.300920272582-0.05717509096220.2432725937683.89296906333-10.1601663351.87648783069
53.34215108498-0.6085678468911.233397230075.25079620904-0.7670132806952.542798972140.0614593833266-0.106554566974-0.3567817572120.3715225179490.0254903728871-0.06188851463270.4290426369710.0161373374901-0.1870721977250.2406085794330.00313287218809-0.003325019606960.09367425728240.00338451429670.0891686918426-5.57740605867-15.73355062499.73664010221
66.16993974751-5.28288464935-0.4709304777924.560840144780.4149403211458.36350778355-0.614217150408-0.156317135416-0.2113853462261.258048761720.493216983625-0.3035820120640.17024135468-0.0360766178862-0.06771823480360.381183553046-0.046289351955-0.07330484482260.1988306715170.0204292985880.221395614604-3.25257390857-20.705937484214.878370528
77.478261933371.792132572671.11964286782.222651873810.7104675544111.313995822970.0919327895828-0.5483672001730.001142061454410.497939810483-0.128947062729-0.04135318564150.176232688701-0.0398301332510.00578069333840.205393579152-0.00621234009005-0.0004992083281470.1217602899010.01754904232740.0890673895727-7.53098337855-9.720444144812.501215313
88.028301815120.7298397361672.584905399076.637562126121.756697606954.3684111964-0.113333956438-0.000850036978361-0.0701241755394-0.04805779819250.226314146348-0.466780560581-0.02291276004170.446724642146-0.1429152577210.1650668191740.0121080260333-0.02762443524560.177177435774-0.006460297581410.1888855138886.40693892674-5.367471553779.77520575582
92.847566593840.5525620933160.8342121919673.910442299850.4727853780182.460518495020.04353567189750.0332801570655-0.2077890277420.2993831155470.0767922930282-0.1772597059410.4023111803890.125393872624-0.09748734720750.182626617030.0140001528496-0.004254485584830.0861213576272-0.006081890208450.0497630559732-5.35536287857-12.28490206145.05184468965
105.596839316941.92176822546-0.8566363939316.618954203990.5418964971927.30442468810.403558647454-0.3496393990990.5777737060850.2145942898580.255109043538-0.0832156026605-0.6196166335211.08032825004-0.1828869489280.218090160922-0.07541206731890.05533722893340.232211202488-0.02274772290670.1795765034271.113717460053.848118240935.03203150845
111.999975914312.000030032741.99999605511.999973951742.000013630328.65834164758-0.588529448857-0.8553591175151.275427152961.117615950011.11565961932-1.95649004954-0.1967677673230.297900975854-0.5231377432020.59985001769-0.346677258192-0.2208643359990.612707478794-0.214597140310.7417582471424.428659790378.989092136048.51470363339
123.74333135870.1137957700123.125281699181.91137915156-0.759767884033.434706694950.09877731976720.707881855597-0.39254510229-0.227858095863-0.03998940812180.0568106101840.2519795412260.658067004642-0.1842893087120.1348201588660.01879533439910.03717242997150.227932417029-0.0009996229927650.138637869106-1.70068570852-2.95005967082-25.0372961287
134.275952460642.745882759380.366488605925.32615777595-0.5933294723495.43034882699-0.04444683247980.188217505734-0.0915280087137-0.05596979941230.181155987228-0.00789004187025-0.182150465015-0.0351829816967-0.04068716059940.09176916900090.01464421645090.02227287654560.1667351146130.02744049814960.132551617691-3.568507280636.03814838214-24.8213782524
141.617647621582.56405782065-1.941037217559.02696744349-6.555909856484.788706846970.05999342222350.06381065124070.1083321295760.289387474371-0.258570268327-0.243752281066-0.2790432897580.2729379373970.1161872542320.124859691977-0.0211412396154-0.002074588960750.1324136462640.0123420901490.111318132472-4.300635019021.53855512853-10.1816280119
153.600941438780.6813703826961.609785770410.2550628339440.1137072349973.660291890660.1617556062940.01390961938620.0835199130670.169081532801-0.1061466328240.3997397455530.120342877591-0.00347903819545-0.07767258830770.09706292185310.004433944784270.01995302229210.0857230797328-0.0198027371870.141939282186-15.5123259441-9.56272576056-10.1486108474
163.119300839391.335481766351.361365156445.175050682280.7716636618283.227681077030.07689814813230.107278057568-0.08000004189170.119516033456-0.0239277083179-0.1184154253350.09536011817180.0937200115149-0.05985559340590.08643386988540.0222509787720.02884307708710.0886449736241-0.003426015547780.0578144430031-8.63390879124-11.7639577774-14.633145739
173.065790612434.986562120441.162578194748.247181618371.750303151574.071435596650.05779818892020.488494069177-0.07118271258-0.1182421777540.01279398909320.0909474401213-0.08591813415-0.0474993481038-0.02113229114770.1733721971830.06180245679920.002103429057730.127704622927-0.02342387031370.112611031319-12.6668534151-17.8906043194-19.7805402142
188.46865119612-5.988275821913.871213696234.3396906275-3.058413459352.737028359090.2980659926560.393544682483-0.369280538904-0.38086989524-0.3958866711730.08399825453630.1751623817470.1052887375510.116130472180.1242018741820.0302154606710.006432362022590.131357018747-0.0212434876910.125468204452-6.23310623514-8.12630204675-18.6528984671
195.906706362331.295235775373.402324104975.58332440763-2.88219992195.310356787990.2030158164910.29635749641-0.247156367659-0.228562961634-0.006282884065170.61036396370.03327232974370.0216495744117-0.2153508670760.1473508889530.0161555100338-0.01835531912610.10881838179-0.0100312790210.15281138668-18.9133081367-1.08724391411-22.8493858327
204.94833492306-0.8831397525683.845849439324.27704960451-2.048993653344.978204606630.185304264231-0.0826060750848-0.102391786653-0.05399368436880.01662184695570.1164881250820.209934380681-0.0751988774025-0.2825620449930.09336778813180.009566198491660.0340015022440.0620833309368-0.00739526782820.0502111827121-11.746325455-13.3395266989-11.6153813086
214.89719123292-0.9660289878880.02260561930276.99320450585-3.415080975965.812203413530.180482255522-0.1041389999580.200729194382-0.1059942432010.04331211740290.47086374186-0.120413688566-0.179693088923-0.1069531130580.109014860822-0.01424781352530.006082994165830.1058328641590.003568388540560.13570277271-8.982136528421.10357919125-12.0504362889
223.718580089271.70709243398-0.5663942078413.78464292084-3.236762504543.04337426170.102626126010.03292774903810.149411946455-0.1714915906250.0881867736370.404748797532-0.468194285507-0.671267975106-0.4138928777640.226077868440.047139001375-0.01137059914490.2494130893550.004359451691530.224491510431-11.8583211168.82874342646-18.1471250751
232.000022783597.77921026448-6.336188202574.27697309239-2.976816800488.56220192068-0.09646234441110.334399410387-0.002394077435880.323410997270.8035506422691.233059782160.168967419594-1.20587300854-0.7282131147120.1229110071260.07545152243690.042063914680.3552273285510.1925156701340.310638765431-10.408630544414.5352382604-23.4117911554
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 95 through 114 )AA95 - 11417 - 36
22chain 'A' and (resid 115 through 123 )AA115 - 12337 - 45
33chain 'A' and (resid 124 through 133 )AA124 - 13346 - 55
44chain 'A' and (resid 134 through 139 )AA134 - 13956 - 61
55chain 'A' and (resid 140 through 153 )AA140 - 15362 - 75
66chain 'A' and (resid 154 through 160 )AA154 - 16076 - 82
77chain 'A' and (resid 161 through 167 )AA161 - 16783 - 89
88chain 'A' and (resid 168 through 175 )AA168 - 17590 - 97
99chain 'A' and (resid 176 through 194 )AA176 - 19498 - 116
1010chain 'A' and (resid 195 through 201 )AA195 - 201117 - 123
1111chain 'A' and (resid 202 through 202 )AA202124
1212chain 'B' and (resid 96 through 102 )BB96 - 10216 - 22
1313chain 'B' and (resid 103 through 114 )BB103 - 11423 - 34
1414chain 'B' and (resid 115 through 123 )BB115 - 12335 - 43
1515chain 'B' and (resid 124 through 139 )BB124 - 13944 - 59
1616chain 'B' and (resid 140 through 153 )BB140 - 15360 - 73
1717chain 'B' and (resid 154 through 160 )BB154 - 16074 - 80
1818chain 'B' and (resid 161 through 167 )BB161 - 16781 - 87
1919chain 'B' and (resid 168 through 176 )BB168 - 17688 - 96
2020chain 'B' and (resid 177 through 188 )BB177 - 18897 - 108
2121chain 'B' and (resid 189 through 194 )BB189 - 194109 - 114
2222chain 'B' and (resid 195 through 201 )BB195 - 201115 - 121
2323chain 'B' and (resid 202 through 204 )BB202 - 204122 - 124

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