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- PDB-1s6i: Ca2+-regulatory region (CLD) from soybean calcium-dependent prote... -

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Basic information

Entry
Database: PDB / ID: 1s6i
TitleCa2+-regulatory region (CLD) from soybean calcium-dependent protein kinase-alpha (CDPK) in the presence of Ca2+ and the junction domain (JD)
ComponentsCalcium-dependent protein kinase SK5
KeywordsTRANSFERASE / PLANT PROTEIN / EF-hand / helix-loop-helix / calcium-binding / calmodulin superfamily
Function / homology
Function and homology information


calcium-dependent protein serine/threonine kinase activity / calcium/calmodulin-dependent protein kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity ...calcium-dependent protein serine/threonine kinase activity / calcium/calmodulin-dependent protein kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / calmodulin binding / intracellular signal transduction / protein serine kinase activity / calcium ion binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
: / EF hand domain / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain ...: / EF hand domain / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calcium-dependent protein kinase SK5
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodSOLUTION NMR / simulated annealing; molecular dynamics; matrix relaxation
AuthorsWeljie, A.M. / Vogel, H.J.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Unexpected structure of the Ca2+-regulatory region from soybean calcium-dependent protein kinase-alpha
Authors: Weljie, A.M. / Vogel, H.J.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Conformational changes in the Ca2+-regulatory region from soybean calcium-dependent protein kinase-alpha: fluorescence resonance energy transfer studies
Authors: Weljie, A.M. / Robertson, K.M. / Vogel, H.J.
#2: Journal: Biochemistry / Year: 2004
Title: Solution Structure and Backbone Dynamics of the N-Terminal Region of the Calcium Regulatory Domain from Soybean Calcium-Dependent Protein Kinase alpha
Authors: Weljie, A.M. / Gagne, S.M. / Vogel, H.J.
#3: Journal: Science / Year: 1991
Title: A calcium-dependent protein kinase with a regulatory domain similar to calmodulin
Authors: Harper, J.F. / Sussman, M.R. / Schaller, G.E. / Putnam-Evans, C. / Charbonneau, H. / Harmon, A.C.
History
DepositionJan 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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 / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium-dependent protein kinase SK5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4215
Polymers21,2611
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations
Representative

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Components

#1: Protein Calcium-dependent protein kinase SK5 / E.C.2.7.1.- / CDPK / calcium-dependent protein kinase-alpha


Mass: 21260.645 Da / Num. of mol.: 1 / Fragment: Calmodulin-like domain (CLD) and C-terminal tail
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean)
Description: Ca2+-binding region and C-terminal tail, along with His(6) at C-terminus
Gene: CDPK SK5 / Plasmid: PT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P28583, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2113D 13C-separated NOESY
2213D 15N-separated NOESY
1313D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM U-15N,13C CLD; 0.9 mM unlabelled JD peptide; 50 mM H2-Imidazole, pH 7.3; 150 mM NaCl; 10 mM CaCl2; 95% H2O, 5% D2O95% H2O/5% D2O
20.5 mM U-15N CLD; 0.6 mM unlabelled JD peptide; 50 mM H2-Imidazole, pH 7.3; 200 mM NaCl; 10 mM CaCl2; 95% H2O, 5% D2O95% H2O/5% D2O
30.5 mM unlabelled CLD; 0.6 mM unlabelled JD peptide; 50 mM H2-Imidazole, pH 7.3; 200 mM NaCl,10 mM CaCl2; 95% H2O, 5% D2O95% H2O/5% D2O
40.4 mM U-15N CLD; 50 mM H2-Imidazole, pH 7.3; 200 mM NaCl; 10 mM CaCl2; 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1200 mM NaCl, 10 mM CaCl2, 50 mM H2-Imidazole 7.3ambient 313 K
2150 mM NaCl, 10 mM CaCl2, 50 mM H2-Imidazole 7.3ambient 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe2.1Delaglio and Baxprocessing
NMRView5.04Johnsondata analysis
CNS1.1Brungerstructure solution
ARIA1.2Nilgesiterative matrix relaxation
VNMRunknownVariancollection
CNS1.1Brungerrefinement
RefinementMethod: simulated annealing; molecular dynamics; matrix relaxation
Software ordinal: 1
Details: Based on 3051 unambiguous NOE-derived restraints, 1183 ambiguous NOE-derived restraints, 122 dihedral angle restraints (TALOS derived), 45 HN residual dipolar coupling restraints
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 15

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