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- PDB-6bg2: Crystal structure of cGMP-dependent protein kinase Ialpha (PKG Ia... -

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Basic information

Entry
Database: PDB / ID: 6bg2
TitleCrystal structure of cGMP-dependent protein kinase Ialpha (PKG Ialpha) catalytic domain in AMP-PNP bound state
ComponentscGMP-dependent protein kinase 1
KeywordsTRANSFERASE / Serine/threonine protein kinases (EC 2.7.11.12)
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 / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / cGMP-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsQin, L. / Sankaran, B. / Kim, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM090161-08 United States
CitationJournal: to be published
Title: Crystal structure of cGMP-dependent protein kinase Ialpha (PKG Ialpha) catalytic domain
Authors: Qin, L. / Sankaran, B. / Casteel, D. / Kim, C.
History
DepositionOct 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)160,35916
Polymers157,8954
Non-polymers2,46412
Water26,2121455
1
A: cGMP-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0904
Polymers39,4741
Non-polymers6163
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)40,0904
Polymers39,4741
Non-polymers6163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: cGMP-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0904
Polymers39,4741
Non-polymers6163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: cGMP-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0904
Polymers39,4741
Non-polymers6163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)165.390, 98.500, 116.424
Angle α, β, γ (deg.)90.00, 133.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 39473.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: AMP-PNP / Source: (gene. exp.) Homo sapiens (human) / Gene: PRKG1, PRKG1B, PRKGR1A, PRKGR1B / Plasmid: pBlueBacHis2A / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13976, cGMP-dependent protein kinase
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1455 / 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: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 23.2% PEG1500, 0.08 M PCTP, pH8.0, 0.5% w/v polyvinylpyrrolidone K15

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.83→47.23 Å / Num. obs: 117904 / % possible obs: 99 % / Redundancy: 4.7 % / CC1/2: 0.999 / Net I/σ(I): 16.8
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 4.8 % / Num. unique obs: 5795 / CC1/2: 0.698 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FJQ

3fjq


Resolution: 1.83→47.231 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2155 1993 1.69 %
Rwork0.188 --
obs0.1884 117874 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.83→47.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10265 0 132 1455 11852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710670
X-RAY DIFFRACTIONf_angle_d0.78214500
X-RAY DIFFRACTIONf_dihedral_angle_d18.4253805
X-RAY DIFFRACTIONf_chiral_restr0.0511576
X-RAY DIFFRACTIONf_plane_restr0.0051834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.87580.2821450.26798187X-RAY DIFFRACTION98
1.8758-1.92650.30811390.25598201X-RAY DIFFRACTION98
1.9265-1.98320.30061380.24248158X-RAY DIFFRACTION98
1.9832-2.04720.24661450.22838272X-RAY DIFFRACTION98
2.0472-2.12040.24891320.22338191X-RAY DIFFRACTION99
2.1204-2.20530.26171530.21718200X-RAY DIFFRACTION99
2.2053-2.30560.26221340.21388260X-RAY DIFFRACTION99
2.3056-2.42720.22661430.2028292X-RAY DIFFRACTION99
2.4272-2.57920.27611370.20278288X-RAY DIFFRACTION99
2.5792-2.77840.24671520.20728327X-RAY DIFFRACTION99
2.7784-3.05790.21181440.19378308X-RAY DIFFRACTION99
3.0579-3.50030.21771450.17698314X-RAY DIFFRACTION99
3.5003-4.40950.16011420.14458371X-RAY DIFFRACTION99
4.4095-47.24640.15861440.15948512X-RAY DIFFRACTION100

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