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- PDB-1kkd: Solution structure of the calmodulin binding domain (CaMBD) of sm... -

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Basic information

Entry
Database: PDB / ID: 1kkd
TitleSolution structure of the calmodulin binding domain (CaMBD) of small conductance Ca2+-activated potassium channels (SK2)
ComponentsSmall conductance calcium-activated potassium channel protein 2
KeywordsSIGNALING PROTEIN / SMALL-CONDUCTANCE CALCIUM-ACTIVATED POTASSIUM CHANNEL / CALMODULIN BINDING DOMAIN (CAMBD) / CHANNEL GATING
Function / homology
Function and homology information


Ca2+ activated K+ channels / small conductance calcium-activated potassium channel activity / membrane repolarization during atrial cardiac muscle cell action potential / calcium-activated potassium channel activity / positive regulation of potassium ion transport / inward rectifier potassium channel activity / regulation of potassium ion transmembrane transport / alpha-actinin binding / smooth endoplasmic reticulum / regulation of neuronal synaptic plasticity ...Ca2+ activated K+ channels / small conductance calcium-activated potassium channel activity / membrane repolarization during atrial cardiac muscle cell action potential / calcium-activated potassium channel activity / positive regulation of potassium ion transport / inward rectifier potassium channel activity / regulation of potassium ion transmembrane transport / alpha-actinin binding / smooth endoplasmic reticulum / regulation of neuronal synaptic plasticity / potassium ion transmembrane transport / T-tubule / sarcolemma / modulation of chemical synaptic transmission / potassium ion transport / Z disc / dendritic spine / postsynaptic membrane / calmodulin binding / protein domain specific binding / neuronal cell body / glutamatergic synapse / cell surface / protein homodimerization activity / membrane / plasma membrane
Similarity search - Function
Calmodulin-binding domain / Potassium channel, calcium-activated, SK / SK, calmodulin-binding domain superfamily / Calmodulin binding domain / Calcium-activated SK potassium channel / Calmodulin binding domain / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins ...Calmodulin-binding domain / Potassium channel, calcium-activated, SK / SK, calmodulin-binding domain superfamily / Calmodulin binding domain / Calcium-activated SK potassium channel / Calmodulin binding domain / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Small conductance calcium-activated potassium channel protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / SIMULATED ANNEALING, TORSION ANGLE DYNAMICS
AuthorsWissmann, R. / Bildl, W. / Neumann, H. / Rivard, A.F. / Kloecker, N. / Weitz, D. / Schulte, U. / Adelman, J.P. / Bentrop, D. / Fakler, B.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: A helical region in the C terminus of small-conductance Ca2+-activated K+ channels controls assembly with apo-calmodulin.
Authors: Wissmann, R. / Bildl, W. / Neumann, H. / Rivard, A.F. / Klocker, N. / Weitz, D. / Schulte, U. / Adelman, J.P. / Bentrop, D. / Fakler, B.
#1: Journal: J.Neurosci. / Year: 1999
Title: Domains responsible for constitutive and Ca2+-dependent interactions between calmodulin and small conductance Ca2+- activated potassium channels
Authors: Keen, J.E. / Khawaled, R. / Farrens, D.L. / Neelands, T. / Rivard, A. / Bond, C.T. / Janowsky, A. / Fakler, B. / Adelman, J.P. / Maylie, J.
#2: Journal: Nature / Year: 1998
Title: Mechanism of calcium gating in small-conductance calcium-activated potassium channels
Authors: Xia, X.-M. / Fakler, B. / Rivard, A. / Wayman, G. / Johnson-Pais, T. / Keen, J.E. / Ishii, T. / Hirschberg, B. / Bond, C.T. / Lutsenko, S. / Maylie, J. / Adelman, J.P.
#3: Journal: Nature / Year: 2001
Title: Structure of the gating domain of a Ca2+-activated K+ channel complexed with Ca2+/calmodulin
Authors: Schumacher, M.A. / Rivard, A.F. / Baechinger, H.P. / Adelman, J.P.
History
DepositionDec 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 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: Small conductance calcium-activated potassium channel protein 2


Theoretical massNumber of molelcules
Total (without water)12,2431
Polymers12,2431
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)23 / 300structures with the least restraint violations,target function
RepresentativeModel #22closest to the average

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Components

#1: Protein Small conductance calcium-activated potassium channel protein 2 / CALCIUM-ACTIVATED POTASSIUM CHANNEL RSK2 / SK2


Mass: 12243.395 Da / Num. of mol.: 1 / Fragment: CYTOPLASMIC CALMODULIN BINDING DOMAIN (CAMBD)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: SK2 (KCNN2) / Plasmid: PET23B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P70604

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2123D 15N-separated NOESY
222HNHA
3332D NOESY
4442D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM U-15N,13C CaMBD (residues 396-487 of rat SK2); 250 mM NaCl, 0.05 % Na-azide90% H2O/10% D2O
21.2 mM U-15N CaMBD (residues 396-487 of rat SK2); 250 mM NaCl, 0.05 % Na-azide90% H2O/10% D2O
31 mM CaMBD (residues 396-487 of rat SK2); 250 mM NaCl, 0.05 % Na-azide90% H2O/10% D2O
41 mM CaMBD (residues 396-487 of rat SK2); 250 mM NaCl, 0.05 % Na-azide100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1250 mM 3.5ambient 298 K
2250 mM 3.5ambient 298 K
3250 mM 3.5ambient 298 K
4250 mM 3.5ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
AURELIA2.7.5Neidigdata analysis
XEASY1.3.13ETH Zuerichdata analysis
DYANA1.5MUMENTHALER, GUENTERTstructure solution
DYANA1.5MUMENTHALER, GUENTERTrefinement
RefinementMethod: SIMULATED ANNEALING, TORSION ANGLE DYNAMICS / Software ordinal: 1
Details: see Table 1 in the primary citation for structural statistics
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations,target function
Conformers calculated total number: 300 / Conformers submitted total number: 23

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