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- PDB-3nmd: Crystal structure of the leucine zipper domain of cGMP dependent ... -

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Basic information

Entry
Database: PDB / ID: 3nmd
TitleCrystal structure of the leucine zipper domain of cGMP dependent protein kinase I beta
ComponentscGMP Dependent PRotein Kinase
KeywordsTRANSFERASE / leucine zipper / coiled-coil / Structural Genomics / Berkeley Structural Genomics Center / BSGC / dimerization / inositol triphosphate receptor-associated PKG substrate / transcriptional regulator TFII-I
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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / 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 ...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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
HEXANE-1,6-DIOL / cGMP-dependent protein kinase 1 / cGMP-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.272 Å
AuthorsKim, C. / Casteel, D.E. / Smith-Nguyen, E.V. / Sankaran, B. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: J.Biol.Chem. / Year: 2010
Title: A crystal structure of the cyclic GMP-dependent protein kinase I{beta} dimerization/docking domain reveals molecular details of isoform-specific anchoring.
Authors: Casteel, D.E. / Smith-Nguyen, E.V. / Sankaran, B. / Roh, S.H. / Pilz, R.B. / Kim, C.
History
DepositionJun 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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
B: cGMP Dependent PRotein Kinase
C: cGMP Dependent PRotein Kinase
D: cGMP Dependent PRotein Kinase
E: cGMP Dependent PRotein Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,55613
Polymers43,6375
Non-polymers9198
Water1,802100
1
A: cGMP Dependent PRotein Kinase
B: cGMP Dependent PRotein Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5733
Polymers17,4552
Non-polymers1181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-30 kcal/mol
Surface area7750 Å2
MethodPISA
2
C: cGMP Dependent PRotein Kinase
D: cGMP Dependent PRotein Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0467
Polymers17,4552
Non-polymers5915
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-15 kcal/mol
Surface area8310 Å2
MethodPISA
3
E: cGMP Dependent PRotein Kinase
hetero molecules

E: cGMP Dependent PRotein Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8756
Polymers17,4552
Non-polymers4214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3520 Å2
ΔGint-18 kcal/mol
Surface area7280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.774, 77.312, 148.616
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
cGMP Dependent PRotein Kinase


Mass: 8727.358 Da / Num. of mol.: 5 / Fragment: Dimerization docking domain, UNP residues 4-55 / Mutation: K41M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKG1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6P5T7, UniProt: Q13976*PLUS
#2: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL / 1,6-Hexanediol


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.06 Å3/Da / Density % sol: 40.35 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M sodium citrate (pH 5.6) and 2.5 mM hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→48 Å / Num. all: 32400 / Num. obs: 32085 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rsym value: 0.074 / Net I/σ(I): 23.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.272→48 Å / SU ML: 1.14 / σ(F): 1.89 / Phase error: 23.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 1620 5.05 %
Rwork0.1946 --
obs0.1973 32085 99.71 %
all-21461 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.449 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.5095 Å2-0 Å20 Å2
2---10.0908 Å2-0 Å2
3---0.5813 Å2
Refinement stepCycle: LAST / Resolution: 2.272→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2152 0 62 100 2314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052220
X-RAY DIFFRACTIONf_angle_d0.7792944
X-RAY DIFFRACTIONf_dihedral_angle_d17.276926
X-RAY DIFFRACTIONf_chiral_restr0.05328
X-RAY DIFFRACTIONf_plane_restr0.002387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2722-2.33910.21551300.17522497X-RAY DIFFRACTION99
2.3391-2.41460.23761480.18042536X-RAY DIFFRACTION100
2.4146-2.50080.22971450.17712549X-RAY DIFFRACTION100
2.5008-2.6010.27491390.18962522X-RAY DIFFRACTION100
2.601-2.71930.27271210.19062538X-RAY DIFFRACTION100
2.7193-2.86270.30891440.20322548X-RAY DIFFRACTION100
2.8627-3.0420.24031180.20662537X-RAY DIFFRACTION100
3.042-3.27690.30251490.19152558X-RAY DIFFRACTION100
3.2769-3.60650.25471240.18892553X-RAY DIFFRACTION100
3.6065-4.12820.17821350.15992562X-RAY DIFFRACTION100
4.1282-5.20010.23031360.18122520X-RAY DIFFRACTION100
5.2001-48.74390.24711310.23332545X-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)
14.7627-0.7809-2.2790.16380.72260.46660.85430.99680.1861-0.3517-0.5570.0273-0.5976-0.3338-0.12390.33940.10710.07470.39160.06510.2915-2.485412.1312.9841
27.0254-1.0627-2.8120.2460.5161.5620.4601-0.8786-0.42930.0085-0.27430.0919-0.14310.3975-0.06740.13770.02030.03450.22630.02380.16090.08568.16927.8533
30.9335-0.37760.33765.2192-0.55750.5061-0.08930.1749-0.00120.40720.29781.04690.0022-0.1878-0.14130.3339-0.01690.01220.29020.01960.2994-12.319929.933219.6791
41.58481.01130.00650.67560.38191.0418-0.03470.0713-0.12380.14810.1034-0.4562-0.0040.0281-0.05730.2604-0.0327-0.03280.21950.01230.1995-5.342929.827522.7931
51.2967-1.15950.03960.95830.44231.2522-0.11140.07380.0993-0.71930.3774-0.3697-0.18370.0658-0.20850.32060.0379-0.08150.1812-0.01460.22911.067337.688333.6967
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E

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