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- PDB-4z07: Co-crystal structure of the tandem CNB (CNB-A/B) domains of human... -

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Basic information

Entry
Database: PDB / ID: 4z07
TitleCo-crystal structure of the tandem CNB (CNB-A/B) domains of human PKG I beta with cGMP
ComponentscGMP-dependent protein kinase 1
KeywordsTRANSFERASE / cGMP-binding domains / cGMP mediated dimeric interface / allosteric regulatory domain / serine-threonine kinase
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
ISOPROPYL ALCOHOL / CYCLIC GUANOSINE MONOPHOSPHATE / cGMP-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKim, J.J. / Reger, A.S. / Arold, S.T. / Kim, C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM090161 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R21 HL111953 United States
CitationJournal: Structure / Year: 2016
Title: Crystal Structure of PKG I:cGMP Complex Reveals a cGMP-Mediated Dimeric Interface that Facilitates cGMP-Induced Activation.
Authors: Kim, J.J. / Lorenz, R. / Arold, S.T. / Reger, A.S. / Sankaran, B. / Casteel, D.E. / Herberg, F.W. / Kim, C.
History
DepositionMar 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)89,93111
Polymers87,9893
Non-polymers1,9428
Water5,945330
1
A: cGMP-dependent protein kinase 1
C: cGMP-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2569
Polymers58,6592
Non-polymers1,5977
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-37 kcal/mol
Surface area25390 Å2
MethodPISA
2
E: cGMP-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6752
Polymers29,3301
Non-polymers3451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.239, 202.978, 134.551
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

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


Mass: 29329.557 Da / Num. of mol.: 3 / Fragment: UNP residues 92-351
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, cGMP-dependent protein kinase
#2: Chemical
ChemComp-PCG / CYCLIC GUANOSINE MONOPHOSPHATE / Cyclic guanosine monophosphate


Mass: 345.205 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H12N5O7P
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M ammonium sulfate, 17.5% PEG 8000 (w/v), 10% Isopropanol, 0.1 M HEPES, pH 8.0

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 24, 2012
RadiationMonochromator: double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 35106 / % possible obs: 99.2 % / Redundancy: 4.1 % / Net I/σ(I): 14.9
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
REFMACrefinement
HKL-3000data scaling
PHASERphasing
HKL-3000phasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3OD0, 4KU7

3od0

4ku7


Resolution: 2.5→36.62 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2237 1551 5 %
Rwork0.1623 --
obs0.1654 31051 87.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→36.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5005 0 128 330 5463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085243
X-RAY DIFFRACTIONf_angle_d1.1417119
X-RAY DIFFRACTIONf_dihedral_angle_d14.2451989
X-RAY DIFFRACTIONf_chiral_restr0.045802
X-RAY DIFFRACTIONf_plane_restr0.006887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.57620.2784900.17711734X-RAY DIFFRACTION57
2.5762-2.66820.2726820.182000X-RAY DIFFRACTION66
2.6682-2.7750.26871110.20042320X-RAY DIFFRACTION76
2.775-2.90130.2851270.20772574X-RAY DIFFRACTION85
2.9013-3.05420.28781610.212753X-RAY DIFFRACTION91
3.0542-3.24540.25961640.19352893X-RAY DIFFRACTION96
3.2454-3.49580.26691660.17652989X-RAY DIFFRACTION99
3.4958-3.84730.20621570.15083046X-RAY DIFFRACTION99
3.8473-4.40320.18251610.12153015X-RAY DIFFRACTION99
4.4032-5.54450.17171690.12813060X-RAY DIFFRACTION99
5.5445-36.62340.19331630.15963116X-RAY DIFFRACTION96
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)
11.887-0.0575-0.75261.5212-0.83532.26310.024-0.1063-0.00840.20950.0787-0.02290.0467-0.0481-0.05680.1713-0.0738-0.03390.15340.03120.151732.5398-15.6591-29.5911
21.0828-0.2683-0.99641.4370.14191.3031-0.0212-0.0484-0.3215-0.0614-0.1548-0.05960.32170.01830.09990.24960.0084-0.00410.18560.03120.278347.3693-32.5129-49.8981
32.93270.186-0.28232.8366-1.10543.9736-0.0407-0.1263-0.18680.06570.0832-0.08150.01520.1918-0.05420.09240.06530.01670.17450.0330.18961.8604-26.1164-64.082
42.44460.5544-1.35261.3603-0.34842.8227-0.13380.1276-0.4569-0.0426-0.0798-0.15440.4972-0.24510.16130.2675-0.0771-0.01880.1918-0.00920.392531.4448-46.154-41.8206
51.00140.5856-0.40151.0946-1.12182.00460.0254-0.01780.04280.11680.02920.1327-0.0198-0.2199-0.05970.2837-0.0733-0.03230.31030.0410.18224.1185-35.4444-8.1034
63.41890.3615-1.13393.0487-0.25192.14580.2016-0.30890.26670.44730.04970.3434-0.0383-0.3483-0.20480.3087-0.09910.0470.42880.0270.218317.5897-37.99762.7314
73.2250.19850.79362.75051.3942.1613-0.0250.05040.218-0.30720.1130.8245-0.2714-0.0921-0.01570.1889-0.0299-0.04970.13340.0220.290121.394-1.3127-44.5361
81.80971.6802-0.67992.09350.46375.5490.1413-0.17760.1544-0.0724-0.27180.4849-0.2062-0.46161.03320.3679-0.0358-0.35760.3737-0.06850.478112.2307-8.5888-53.8064
91.12890.29921.15811.7520.28491.17560.01-0.0784-0.0922-0.16430.0801-0.16610.0133-0.0803-0.09120.1371-0.0822-0.00380.160.00650.228727.1412-9.6585-48.9035
102.05090.86210.08111.97760.21161.0318-0.14970.2235-0.2402-0.4872-0.06020.09220.0479-0.01280.0560.2873-0.1262-0.13450.2340.00280.200326.9112-15.2754-57.8719
113.2438-1.2682-1.52443.28450.09443.2914-0.1187-0.2519-0.35540.30970.11530.51990.4318-0.4977-0.0470.2732-0.1377-0.05810.25970.01810.275621.1833-10.6377-43.7011
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 92:208 )A92 - 208
2X-RAY DIFFRACTION2( CHAIN A AND RESID 209:257 )A209 - 257
3X-RAY DIFFRACTION3( CHAIN A AND RESID 258:351 )A258 - 351
4X-RAY DIFFRACTION4( CHAIN C AND RESID 94:217 )C94 - 217
5X-RAY DIFFRACTION5( CHAIN C AND RESID 218:271 )C218 - 271
6X-RAY DIFFRACTION6( CHAIN C AND RESID 272:351 )C272 - 351
7X-RAY DIFFRACTION7( CHAIN E AND RESID 92:115 )E92 - 115
8X-RAY DIFFRACTION8( CHAIN E AND RESID 116:123 )E116 - 123
9X-RAY DIFFRACTION9( CHAIN E AND RESID 124:160 )E124 - 160
10X-RAY DIFFRACTION10( CHAIN E AND RESID 161:201 )E161 - 201
11X-RAY DIFFRACTION11( CHAIN E AND RESID 202:217 )E202 - 217

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