[English] 日本語
Yorodumi
- PDB-6mie: Solution NMR structure of the KCNQ1 voltage-sensing domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mie
TitleSolution NMR structure of the KCNQ1 voltage-sensing domain
ComponentsPotassium voltage-gated channel subfamily KQT member 1
KeywordsMEMBRANE PROTEIN / ion channel / KCNQ1 / Kv7.1 / voltage sensor / potassium channel
Function / homology
Function and homology information


gastrin-induced gastric acid secretion / stomach development / corticosterone secretion / voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization / negative regulation of voltage-gated potassium channel activity / basolateral part of cell / lumenal side of membrane / negative regulation of delayed rectifier potassium channel activity / rhythmic behavior / regulation of gastric acid secretion ...gastrin-induced gastric acid secretion / stomach development / corticosterone secretion / voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization / negative regulation of voltage-gated potassium channel activity / basolateral part of cell / lumenal side of membrane / negative regulation of delayed rectifier potassium channel activity / rhythmic behavior / regulation of gastric acid secretion / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / Phase 3 - rapid repolarisation / membrane repolarization during action potential / auditory receptor cell development / membrane repolarization during atrial cardiac muscle cell action potential / iodide transport / Phase 2 - plateau phase / intracellular chloride ion homeostasis / regulation of atrial cardiac muscle cell membrane repolarization / membrane repolarization during ventricular cardiac muscle cell action potential / atrial cardiac muscle cell action potential / renal sodium ion absorption / potassium ion export across plasma membrane / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of membrane repolarization / detection of mechanical stimulus involved in sensory perception of sound / membrane repolarization during cardiac muscle cell action potential / protein phosphatase 1 binding / potassium ion homeostasis / intestinal absorption / delayed rectifier potassium channel activity / ventricular cardiac muscle cell action potential / non-motile cilium assembly / regulation of ventricular cardiac muscle cell membrane repolarization / positive regulation of potassium ion transmembrane transport / inner ear morphogenesis / Voltage gated Potassium channels / outward rectifier potassium channel activity / regulation of heart contraction / cardiac muscle cell contraction / adrenergic receptor signaling pathway / inner ear development / monoatomic ion channel complex / renal absorption / protein kinase A regulatory subunit binding / ciliary base / protein kinase A catalytic subunit binding / regulation of heart rate by cardiac conduction / social behavior / potassium ion import across plasma membrane / cochlea development / action potential / voltage-gated potassium channel activity / positive regulation of heart rate / cardiac muscle contraction / transport vesicle / sensory perception of sound / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of cardiac muscle contraction / voltage-gated potassium channel complex / cellular response to epinephrine stimulus / cellular response to cAMP / potassium ion transmembrane transport / erythrocyte differentiation / cytoplasmic vesicle membrane / cellular response to xenobiotic stimulus / glucose metabolic process / response to insulin / regulation of membrane potential / regulation of blood pressure / heart development / late endosome / scaffold protein binding / basolateral plasma membrane / early endosome / transmembrane transporter binding / calmodulin binding / lysosome / apical plasma membrane / neuron projection / membrane raft / ubiquitin protein ligase binding / neuronal cell body / endoplasmic reticulum / membrane / plasma membrane / cytoplasm
Similarity search - Function
Potassium channel, voltage dependent, KCNQ1 / Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily KQT member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsTaylor, K.C. / Kuenze, G. / Smith, J.A. / Meiler, J. / McFeeters, R.L. / Sanders, C.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)RO1 HL122010 United States
CitationJournal: Elife / Year: 2020
Title: Structure and physiological function of the human KCNQ1 channel voltage sensor intermediate state.
Authors: Taylor, K.C. / Kang, P.W. / Hou, P. / Yang, N.D. / Kuenze, G. / Smith, J.A. / Shi, J. / Huang, H. / White, K.M. / Peng, D. / George, A.L. / Meiler, J. / McFeeters, R.L. / Cui, J. / Sanders, C.R.
History
DepositionSep 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Potassium voltage-gated channel subfamily KQT member 1


Theoretical massNumber of molelcules
Total (without water)18,1851
Polymers18,1851
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10090 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 150structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein Potassium voltage-gated channel subfamily KQT member 1 / IKs producing slow voltage-gated potassium channel subunit alpha KvLQT1 / KQT-like 1 / Voltage- ...IKs producing slow voltage-gated potassium channel subunit alpha KvLQT1 / KQT-like 1 / Voltage-gated potassium channel subunit Kv7.1


Mass: 18184.631 Da / Num. of mol.: 1 / Fragment: UNP residues 100-249
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNQ1, KCNA8, KCNA9, KVLQT1 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) pRARE / References: UniProt: P51787

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D HNCA
121isotropic23D HNCO
131isotropic23D HN(CO)CA
141isotropic23D 1H-15N NOESY
151isotropic23D HN(CA)CB
161isotropic22D 1H-15N HSQC
172isotropic12D 1H-15N HSQC
182isotropic13D H(CCO)NH
192isotropic13D C(CO)NH
1102isotropic13D (H)CCH-COSY
1113isotropic22D 1H-13C HSQC aliphatic
1123isotropic23D 1H-13C NOESY
1134isotropic22D 1H-15N HSQC
1144isotropic23D 1H-15N NOESY
1154isotropic22D IPAP-HSQC
1165anisotropic22D IPAP-HSQC
1176isotropic22D 1H-15N HSQC
1187isotropic22D 1H-15N HSQC
1198isotropic22D 1H-15N HSQC
1209isotropic22D 1H-15N HSQC
12110isotropic22D 1H-15N HSQC
12211isotropic22D 1H-15N HSQC
12312isotropic22D 1H-15N HSQC
12413isotropic22D 1H-15N HSQC

-
Sample preparation

Details
TypeSolution-IDContentsDetails (eV)LabelSolvent system
micelle10.4 mM [U-100% 13C; U-100% 15N; U-80% 2H] KCNQ1-VSD, 50 mM MES, 0.5 mM EDTA, 2 mM TCEP, 4 % w/v LMPG, 95% H2O/5% D2O13C-15N specific labeled sample was grown in M9 culture with 99% D2O. After purification, the sample was exchanged into 50 mM MES buffer (pH5.50), 5% D2O, 0.5 mM EDTA and 2 mM TCEP.Q1-VSD 2H13C15N95% H2O/5% D2O
micelle20.4 mM [U-100% 13C; U-100% 15N] KCNQ1-VSD, 50 mM MES, 0.5 mM EDTA, 2 mM TCEP, 4 % w/v LMPG, 95% H2O/5% D2O13C-15N specific labeled sample was grown in M9 culture. After purification, the sample was exchanged into 50 mM MES buffer pH 5.50, 5% D2O, 0.5 mM EDTA and 2 mM TCEP.Q1-VSD 13C15N95% H2O/5% D2O
micelle30.4 mM [U-100% 13C; U-100% 15N] KCNQ1-VSD, 50 mM MES, 0.5 mM EDTA, 2 mM TCEP, 4 % w/v Deuterated LMPG, 100% D2O13C-15N specific labeled sample was grown in M9. After purification, the sample was exchanged into 50 mM MES buffer (pH5.50), 5% D2O, 0.5 mM EDTA and 2 mM TCEP. Deuterated LMPG was used for this sample.Q1-VSD 13C15N + deuterated LMPG100% D2O
micelle40.4 mM [U-100% 15N] KCNQ1-VSD, 50 mM MES, 0.5 mM EDTA, 2 mM TCEP, 4 % w/v LMPG, 95% H2O/5% D2O15N specific labeled sample was grown in M9. After purification, the sample was exchanged into 50 mM MES buffer (pH5.50), 5% D2O, 0.5 mM EDTA and 2 mM TCEP.Q1-VSD 15N95% H2O/5% D2O
micelle50.2 mM [U-100% 15N] KCNQ1-VSD, 50 mM MES, 0.5 mM EDTA, 2 mM TCEP, 4 mM LMPG, 95% H2O/5% D2O15N specific labeled sample was grown in M9. After purification, the sample was exchanged into 50 mM MES buffer (pH5.50), 5% D2O, 0.5 mM EDTA and 2 mM TCEP. Anisotropic sample was soaked into a 6 mm 5% gel and stretched into a 5 mm open ended NMR tube.Q1-VSD 15N anisotropic95% H2O/5% D2O
micelle60.2 mM [U-100% 15N] KCNQ1-VSD, 50 mM MES, 0.5 mM EDTA, 2 mM TCEP, 4 mM LMPG, 95% H2O/5% D2OK121C-MTSL, C122S, C136A, C180S, C214AQ1-VSD 15N K121C-MTSL95% H2O/5% D2O
bicelle70.2 mM [U-100% 15N] KCNQ1-VSD, 50 mM MES, 0.5 mM EDTA, 2 mM TCEP, 4 % w/v LMPG, 95% H2O/5% D2OT144C-MTSL, C122S, C136A, C180S, C214AQ1-VSD 15N T144C-MTSL95% H2O/5% D2O
micelle80.2 mM [U-100% 15N] KCNQ1-VSD, 50 mM MES, 0.5 mM EDTA, 2 mM TCEP, 4 % w/v LMPG, 95% H2O/5% D2OT155C-MTSL, C122S, C136A, C180S, C214AQ1-VSD 15N T155C-MTSL95% H2O/5% D2O
micelle90.2 mM [U-100% 15N] KCNQ1-VSD, 50 mM MES, 0.5 mM EDTA, 2 mM TCEP, 4 % w/v LMPG, 95% H2O/5% D2OT177C-MTSL, C122S, C136A, C180S, C214AQ1-VSD 15N T177C-MTSL95% H2O/5% D2O
micelle100.2 mM [U-100% 15N] KCNQ1-VSD, 50 mM MES, 0.5 mM EDTA, 2 mM TCEP, 4 % w/v LMPG, 95% H2O/5% D2OC180-MTSL, C122S, C136A, C214AQ1-VSD 15N C180-MTSL95% H2O/5% D2O
micelle110.2 mM [U-100% 15N] KCNQ1-VSD, 50 mM MES, 0.5 mM EDTA, 2 mM TCEP, 4 % w/v LMPG, 95% H2O/5% D2OC214-MTSL, C122S, C136A, C180SQ1-VSD 15N C214-MTSL95% H2O/5% D2O
micelle120.2 mM [U-100% 15N] KCNQ1-VSD, 50 mM MES, 0.5 mM EDTA, 2 mM TCEP, 4 % w/v LMPG, 95% H2O/5% D2OT224C-MTSL, C122S, C136A, C180S, C214AQ1-VSD 15N T224C-MTSL95% H2O/5% D2O
micelle130.2 mM [U-100% 15N] KCNQ1-VSD, 50 mM MES, 0.5 mM EDTA, 2 mM TCEP, 4 % w/v LMPG, 95% H2O/5% D2OM238C-MTSL, C122S, C136A, C180S, C214AQ1-VSD 15N M238C-MTSL95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMKCNQ1-VSD[U-100% 13C; U-100% 15N; U-80% 2H]1
50 mMMESnatural abundance1
0.5 mMEDTAnatural abundance1
2 mMTCEPnatural abundance1
4 % w/vLMPGnatural abundance1
0.4 mMKCNQ1-VSD[U-100% 13C; U-100% 15N]2
50 mMMESnatural abundance2
0.5 mMEDTAnatural abundance2
2 mMTCEPnatural abundance2
4 % w/vLMPGnatural abundance2
0.4 mMKCNQ1-VSD[U-100% 13C; U-100% 15N]3
50 mMMESnatural abundance3
0.5 mMEDTAnatural abundance3
2 mMTCEPnatural abundance3
4 % w/vDeuterated LMPGnatural abundance3
0.4 mMKCNQ1-VSD[U-100% 15N]4
50 mMMESnatural abundance4
0.5 mMEDTAnatural abundance4
2 mMTCEPnatural abundance4
4 % w/vLMPGnatural abundance4
0.2 mMKCNQ1-VSD[U-100% 15N]5
50 mMMESnatural abundance5
0.5 mMEDTAnatural abundance5
2 mMTCEPnatural abundance5
4 mMLMPGnatural abundance5
0.2 mMKCNQ1-VSD[U-100% 15N]6
50 mMMESnatural abundance6
0.5 mMEDTAnatural abundance6
2 mMTCEPnatural abundance6
4 mMLMPGnatural abundance6
0.2 mMKCNQ1-VSD[U-100% 15N]7
50 mMMESnatural abundance7
0.5 mMEDTAnatural abundance7
2 mMTCEPnatural abundance7
4 % w/vLMPGnatural abundance7
0.2 mMKCNQ1-VSD[U-100% 15N]8
50 mMMESnatural abundance8
0.5 mMEDTAnatural abundance8
2 mMTCEPnatural abundance8
4 % w/vLMPGnatural abundance8
0.2 mMKCNQ1-VSD[U-100% 15N]9
50 mMMESnatural abundance9
0.5 mMEDTAnatural abundance9
2 mMTCEPnatural abundance9
4 % w/vLMPGnatural abundance9
0.2 mMKCNQ1-VSD[U-100% 15N]10
50 mMMESnatural abundance10
0.5 mMEDTAnatural abundance10
2 mMTCEPnatural abundance10
4 % w/vLMPGnatural abundance10
0.2 mMKCNQ1-VSD[U-100% 15N]11
50 mMMESnatural abundance11
0.5 mMEDTAnatural abundance11
2 mMTCEPnatural abundance11
4 % w/vLMPGnatural abundance11
0.2 mMKCNQ1-VSD[U-100% 15N]12
50 mMMESnatural abundance12
0.5 mMEDTAnatural abundance12
2 mMTCEPnatural abundance12
4 % w/vLMPGnatural abundance12
0.2 mMKCNQ1-VSD[U-100% 15N]13
50 mMMESnatural abundance13
0.5 mMEDTAnatural abundance13
2 mMTCEPnatural abundance13
4 % w/vLMPGnatural abundance13
Sample conditionsDetails: A shape tube was used for all 3D experiments. / Ionic strength: 4 % (w/v) LMPG Not defined / Label: conditions_1 / pH: 5.5 / Pressure: 1 atm / Temperature: 323 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails (eV)
Bruker AVANCE IIIBrukerAVANCE III6001CPQCI probe
Bruker AVANCE IIIBrukerAVANCE III9002CPTCI probe

-
Processing

NMR software
NameVersionDeveloperClassification
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
XPLOR-NIH2.48C.D. Schwieters, J.J. Kuszewski, N. Tjandra and G.M. Clorestructure calculation
SparkyNMRFAMGoddardchemical shift assignment
SparkyNMRFAMGoddardpeak picking
TopSpin3.2Bruker Biospincollection
TopSpin3.2Bruker Biospinprocessing
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: 10 structures were solvated in an explicit hydrated DMPC bilayer and 100 ns of restrained molecular dynamics (rMD) were performed. Each trajectory was then extended another 190 ns with NMR ...Details: 10 structures were solvated in an explicit hydrated DMPC bilayer and 100 ns of restrained molecular dynamics (rMD) were performed. Each trajectory was then extended another 190 ns with NMR restraints turned off. The last 100 ns of the trajectory seeded with the lowest energy rMD structure was divided into ten 10 ns blocks. The centroid of the most populated cluster for each 10 ns time block corresponds to models 1 through 10 in the ensemble. Model number 1 has the lowest RMSD to the average coordinates. Each model in the ensemble was scored with the NMR restraints and found to be largely consistent with the experimental data. It is important to note that the precision of the ensemble no longer is reflective of the precision of the XplorNIH simulated annealing step. Please see published methods for further details.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 10

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more