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- PDB-1wgp: Solution structure of the cNMP-binding domain from Arabidopsis th... -

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Basic information

Entry
Database: PDB / ID: 1wgp
TitleSolution structure of the cNMP-binding domain from Arabidopsis thaliana cyclic nucleotide-regulated ion channel
ComponentsProbable cyclic nucleotide-gated ion channel 6
KeywordsMEMBRANE PROTEIN / cyclic nucleotide monophosphate / cNMP / cNMP-binding / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


root hair / intracellularly cGMP-activated cation channel activity / cGMP binding / voltage-gated potassium channel activity / cAMP binding / cell periphery / calcium channel activity / response to heat / calmodulin binding / plasma membrane
Similarity search - Function
Potassium channel, voltage-dependent, EAG/ELK/ERG / IQ motif profile. / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Ion transport domain ...Potassium channel, voltage-dependent, EAG/ELK/ERG / IQ motif profile. / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Ion transport domain / Ion transport protein / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Probable cyclic nucleotide-gated ion channel 6
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsChikayama, E. / Nameki, N. / Kigawa, T. / Koshiba, S. / Inoue, M. / Tomizawa, T. / Kobayashi, N. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the cNMP-binding domain from Arabidopsis thaliana cyclic nucleotide-regulated ion channel
Authors: Chikayama, E. / Nameki, N. / Kigawa, T. / Koshiba, S. / Inoue, M. / Tomizawa, T. / Kobayashi, N. / Yokoyama, S.
History
DepositionMay 28, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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_oper_list / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 700SHEET determination method: author determined

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Structure visualization

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Assembly

Deposited unit
A: Probable cyclic nucleotide-gated ion channel 6


Theoretical massNumber of molelcules
Total (without water)15,0881
Polymers15,0881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations, structures with the lowest energy, target function
Representative

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Components

#1: Protein Probable cyclic nucleotide-gated ion channel 6 / cyclic nucleotide-regulated ion channel / AtCNGC6 / Cyclic nucleotide- and calmodulin-regulated ion channel 6


Mass: 15088.034 Da / Num. of mol.: 1 / Fragment: cNMP binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Description: Cell-free protein synthesis / Gene: RIKEN RAFL05-10-A11 / Plasmid: P021218-34 / References: UniProt: O82226

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 0.66mM cNMP-binding domain U-15N, 13C; 20mM d-Tris-HCl(pH 7.5); 200mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 220mM / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.901Kobayashi, N.data analysis
CYANA2.0.17Guentert, P.structure solution
CYANA2.0.17Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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