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- PDB-2kxl: Solution structure of a bacterial cyclic nucleotide-activated K+ ... -

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Basic information

Entry
Database: PDB / ID: 2kxl
TitleSolution structure of a bacterial cyclic nucleotide-activated K+ channel binding domain in the unliganded state
ComponentsCyclic nucleotide-gated potassium channel mll3241
KeywordsMEMBRANE PROTEIN / Cyclic Nucleotide Binding Domain (CNBD) / Ion Channel / Protein Phosphate Binding Cassette in the Apo State / helical portion / beta barrel core
Function / homology
Function and homology information


intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / intracellularly cAMP-activated cation channel activity / potassium channel activity / cGMP binding / cAMP binding / protein-containing complex binding / identical protein binding / plasma membrane
Similarity search - Function
Cyclic nucleotide-regulated ion channel, N-terminal / 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 / Jelly Rolls ...Cyclic nucleotide-regulated ion channel, N-terminal / 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 / Jelly Rolls / RmlC-like jelly roll fold / Ion transport domain / Ion transport protein / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cyclic nucleotide-gated potassium channel mll3241
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailsfewest violations, model 15
AuthorsSchunke, S. / Stoldt, M. / Willbold, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural insights into conformational changes of a cyclic nucleotide-binding domain in solution from Mesorhizobium loti K1 channel.
Authors: Schunke, S. / Stoldt, M. / Lecher, J. / Kaupp, U.B. / Willbold, D.
History
DepositionMay 10, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclic nucleotide-gated potassium channel mll3241


Theoretical massNumber of molelcules
Total (without water)14,9831
Polymers14,9831
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)15 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Cyclic nucleotide-gated potassium channel mll3241 / MlotiK1 channel


Mass: 14983.222 Da / Num. of mol.: 1 / Fragment: UNP Residues 216-355
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Gene: mll3241 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysE / References: UniProt: Q98GN8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D HN(CA)CB
1423D HNCO
1523D HNHA
1623D (H)CCH-TOCSY
1723D (H)CCH-COSY
1813D 1H-15N NOESY
1923D 1H-13C NOESY
11022D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-15N] MloK1 CNBD, 10 mM [U-99% 2H] TRIS, 100 mM sodium chloride, 0.02 % sodium azide, 5 % [U-100% 2H] D2O, 95 % H2O, 200 uM EDTA, 95% H2O/5% D2O95% H2O/5% D2O
20.5 mM [U-13C; U-15N] MloK1 CNBD, 10 mM [U-99% 2H] TRIS, 100 mM sodium chloride, 0.02 % sodium azide, 5 % [U-100% 2H] D2O, 95 % H2O, 200 uM EDTA, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMMloK1 CNBD-1[U-15N]1
10 mMTRIS-2[U-99% 2H]1
100 mMsodium chloride-31
0.02 %sodium azide-41
5 %D2O-5[U-100% 2H]1
95 %H2O-61
200 uMEDTA-71
0.5 mMMloK1 CNBD-8[U-13C; U-15N]2
10 mMTRIS-9[U-99% 2H]2
100 mMsodium chloride-102
0.02 %sodium azide-112
5 %D2O-12[U-100% 2H]2
95 %H2O-132
200 uMEDTA-142
Sample conditionspH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker INOVABrukerINOVA8001
Bruker INOVABrukerINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARAKeller and Wuthrichpeak picking
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichdata analysis
CYANA1.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA1.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2380 / NOE intraresidue total count: 665 / NOE long range total count: 632 / NOE medium range total count: 456 / NOE sequential total count: 627
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 15 / Maximum upper distance constraint violation: 0.17 Å
NMR ensemble rmsDistance rms dev error: 0.02 Å

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