[English] 日本語
Yorodumi- PDB-2k21: NMR structure of human KCNE1 in LMPG micelles at pH 6.0 and 40 de... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2k21 | ||||||
---|---|---|---|---|---|---|---|
Title | NMR structure of human KCNE1 in LMPG micelles at pH 6.0 and 40 degree C | ||||||
Components | Potassium voltage-gated channel subfamily E member | ||||||
Keywords | MEMBRANE PROTEIN / KCNE1 / potassium channel / MinK / auxilliary subunit / micelles / Ion transport / Ionic channel / Potassium transport / Transmembrane / Transport / Voltage-gated channel | ||||||
Function / homology | Function and homology information negative regulation of protein targeting to membrane / regulation of delayed rectifier potassium channel activity / Phase 3 - rapid repolarisation / membrane repolarization during action potential / membrane repolarization during ventricular cardiac muscle cell action potential / Phase 2 - plateau phase / telethonin binding / potassium ion export across plasma membrane / membrane repolarization during cardiac muscle cell action potential / negative regulation of delayed rectifier potassium channel activity ...negative regulation of protein targeting to membrane / regulation of delayed rectifier potassium channel activity / Phase 3 - rapid repolarisation / membrane repolarization during action potential / membrane repolarization during ventricular cardiac muscle cell action potential / Phase 2 - plateau phase / telethonin binding / potassium ion export across plasma membrane / membrane repolarization during cardiac muscle cell action potential / negative regulation of delayed rectifier potassium channel activity / membrane repolarization / delayed rectifier potassium channel activity / cardiac conduction / positive regulation of potassium ion transmembrane transport / cardiac muscle cell action potential involved in contraction / ventricular cardiac muscle cell action potential / regulation of potassium ion transmembrane transport / regulation of ventricular cardiac muscle cell membrane repolarization / regulation of heart rate by cardiac conduction / voltage-gated potassium channel activity / potassium channel regulator activity / voltage-gated potassium channel complex / cellular response to cAMP / potassium ion transmembrane transport / sensory perception of sound / Z disc / transmembrane transporter binding / lysosome / apical plasma membrane / membrane raft / cell surface / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | ||||||
Model details | Structure of human KCNE1 (also known as MinK) in LMPG micelles. KCNE1 modulates certain voltage- ...Structure of human KCNE1 (also known as MinK) in LMPG micelles. KCNE1 modulates certain voltage-gated potassium channels. | ||||||
Authors | Kang, C. / Tian, C. / Sonnichsen, F.D. / Smith, J.A. / Meiler, J. / George, A.L. / Vanoye, C.G. / Sanders, C.R. / Kim, H. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Structure of KCNE1 and implications for how it modulates the KCNQ1 potassium channel. Authors: Kang, C. / Tian, C. / Sonnichsen, F.D. / Smith, J.A. / Meiler, J. / George, A.L. / Vanoye, C.G. / Kim, H.J. / Sanders, C.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2k21.cif.gz | 406.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2k21.ent.gz | 349.5 KB | Display | PDB format |
PDBx/mmJSON format | 2k21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/2k21 ftp://data.pdbj.org/pub/pdb/validation_reports/k2/2k21 | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 15706.869 Da / Num. of mol.: 1 / Mutation: R104K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KCNE1 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RP / References: UniProt: Q6FHJ6, UniProt: P15382*PLUS |
---|---|
Sequence details | THESE COORDINATES ARE FOR THE R104K MUTANT FORM OF KCNE1, WHICH WAS GENERATED AT AN EARLY STAGE IN ...THESE COORDINATE |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||||||||||||||||||
NMR details | Text: The structure was determined using combination of NOEs, PREs, and RDCs. |
-Sample preparation
Details |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sample conditions | Ionic strength: 0.25 / pH: 6.0 / Pressure: ambient / Temperature: 313 K |
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: DGSA-distance geometry simulated annealing / Software ordinal: 1 Details: The refinement protocol consisted of slow cooling from 1000 K to 100 K spanning 45 ps. Final structures were energy-minimized using 250 steps of Powell energy minimization. The 20 structures ...Details: The refinement protocol consisted of slow cooling from 1000 K to 100 K spanning 45 ps. Final structures were energy-minimized using 250 steps of Powell energy minimization. The 20 structures with lowest energy were subjected to further analysis and spin-labeled Cys residues associated with PRE restraints were changed back to their wild type residues. Powell energy minimization was then performed. | ||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 737 / NOE intraresidue total count: 126 / NOE long range total count: 464 / NOE medium range total count: 50 / NOE sequential total count: 97 / Hydrogen bond constraints total count: 72 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 113 / Protein psi angle constraints total count: 112 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||
NMR ensemble | Average torsion angle constraint violation: 0.2 ° Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 500 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.137 Å / Maximum torsion angle constraint violation: 4.569 ° / Maximum upper distance constraint violation: 0.129 Å / Torsion angle constraint violation method: XPLOR | ||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.008 Å / Distance rms dev error: 0.0019 Å |