[English] 日本語
Yorodumi
- PDB-2m0q: Solution NMR analysis of intact KCNE2 in detergent micelles demon... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2m0q
TitleSolution NMR analysis of intact KCNE2 in detergent micelles demonstrate a straight transmembrane helix
ComponentsPotassium voltage-gated channel subfamily E member 2
KeywordsMEMBRANE PROTEIN / Transmembrane helix / detergent micelle
Function / homology
Function and homology information


regulation of cyclic nucleotide-gated ion channel activity / positive regulation of voltage-gated calcium channel activity / regulation of inward rectifier potassium channel activity / cellular response to xenobiotic stimulus => GO:0071466 / 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 ...regulation of cyclic nucleotide-gated ion channel activity / positive regulation of voltage-gated calcium channel activity / regulation of inward rectifier potassium channel activity / cellular response to xenobiotic stimulus => GO:0071466 / 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 / negative regulation of delayed rectifier potassium channel activity / potassium ion export across plasma membrane / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of membrane repolarization / membrane repolarization / cardiac conduction / positive regulation of proteasomal protein catabolic process / inward rectifier potassium channel activity / ventricular cardiac muscle cell action potential / cardiac muscle cell action potential involved in contraction / regulation of potassium ion transmembrane transport / regulation of ventricular cardiac muscle cell membrane repolarization / delayed rectifier potassium channel activity / tongue development / regulation of heart rate by cardiac conduction / potassium ion import across plasma membrane / potassium channel regulator activity / potassium ion transmembrane transport / voltage-gated potassium channel complex / transmembrane transporter binding / lysosome / Golgi apparatus / cell surface / endoplasmic reticulum / identical protein binding / plasma membrane
Similarity search - Function
Potassium channel, voltage-dependent, beta subunit, KCNE2 / Potassium channel, voltage-dependent, beta subunit, KCNE / Slow voltage-gated potassium channel
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily E member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLai, C. / Li, P. / Chen, L. / Zhang, L. / Wu, F. / Tian, C.
CitationJournal: Sci Rep / Year: 2014
Title: Differential modulations of KCNQ1 by auxiliary proteins KCNE1 and KCNE2.
Authors: Li, P. / Liu, H. / Lai, C. / Sun, P. / Zeng, W. / Wu, F. / Zhang, L. / Wang, S. / Tian, C. / Ding, J.
History
DepositionNov 1, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_nmr_software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Potassium voltage-gated channel subfamily E member 2


Theoretical massNumber of molelcules
Total (without water)14,4861
Polymers14,4861
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)10 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein Potassium voltage-gated channel subfamily E member 2 / MinK-related peptide 1 / Minimum potassium ion channel-related peptide 1 / Potassium channel ...MinK-related peptide 1 / Minimum potassium ion channel-related peptide 1 / Potassium channel subunit beta MiRP1


Mass: 14486.493 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNE2 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6J6

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1332D 1H-15N HSQC
1433D HNCO
1533D HNCA
1633D HN(CO)CA
1733D HN(CA)CB
1833D HN(COCA)CB
1923D HBHA(CO)NH
11013D 1H-15N NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-15N] KCNE2, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-13C; U-15N] KCNE2, 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM [U-13C; U-15N; U-2H] KCNE2, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMKCNE2-1[U-15N]1
1.0 mMKCNE2-4[U-13C; U-15N]2
1.0 mMKCNE2-7[U-13C; U-15N; U-2H]3
Sample conditionsIonic strength: 50 / pH: 6.0 / Pressure: ambient / Temperature: 308 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX8002

-
Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRViewJohnson, One Moon Scientificchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 282 / NOE intraresidue total count: 130 / NOE long range total count: 0 / NOE medium range total count: 21 / NOE sequential total count: 131 / Protein phi angle constraints total count: 120 / Protein psi angle constraints total count: 120
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / 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://pdbjlvh1.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