[English] 日本語
Yorodumi
- PDB-1jo6: Solution structure of the cytoplasmic N-terminus of the BK beta-s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jo6
TitleSolution structure of the cytoplasmic N-terminus of the BK beta-subunit KCNMB2
Componentspotassium large conductance calcium-activated channel, subfamily M, beta member 2
KeywordsMETAL TRANSPORT / MEMBRANE PROTEIN / helix / ion channel / cytoplasmic part of
Function / homology
Function and homology information


Ca2+ activated K+ channels / calcium-activated potassium channel activity / ion channel inhibitor activity / action potential / cGMP effects / regulation of vasoconstriction / detection of calcium ion / neuronal action potential / potassium channel regulator activity / voltage-gated potassium channel complex ...Ca2+ activated K+ channels / calcium-activated potassium channel activity / ion channel inhibitor activity / action potential / cGMP effects / regulation of vasoconstriction / detection of calcium ion / neuronal action potential / potassium channel regulator activity / voltage-gated potassium channel complex / potassium ion transport / plasma membrane
Similarity search - Function
KCNMB2, ball/chain domain / KCNMB2, ball/chain domain / KCNMB2, ball/chain domain superfamily / KCNMB2, ball and chain domain / Potassium channel, calcium-activated, BK, beta subunit / Calcium-activated potassium channel, beta subunit / Cytochrome C Oxidase; Chain M / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Calcium-activated potassium channel subunit beta-2
Similarity search - Component
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsBentrop, D. / Beyermann, M. / Wissmann, R. / Fakler, B.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: NMR structure of the "ball-and-chain" domain of KCNMB2, the beta 2-subunit of large conductance Ca2+- and voltage-activated potassium channels.
Authors: Bentrop, D. / Beyermann, M. / Wissmann, R. / Fakler, B.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Molecular basis of fast inactivation in voltage and Ca2+-activated K+ channels: a transmembrane beta-subunit homolog
Authors: Wallner, M. / Meera, P. / Toro, L.
#2: Journal: J.Neurosci. / Year: 1999
Title: Molecular basis for the inactivation of Ca2+- and voltage-dependent BK channels in adrenal chromaffin cells and rat insulinoma tumor cells
Authors: Xia, X.M. / Ding, J.P. / Lingle, C.J.
History
DepositionJul 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 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
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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: potassium large conductance calcium-activated channel, subfamily M, beta member 2


Theoretical massNumber of molelcules
Total (without water)5,3801
Polymers5,3801
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)24 / 30structures with the least restraint violations,target function
RepresentativeModel #1fewest violations

-
Components

#1: Protein/peptide potassium large conductance calcium-activated channel, subfamily M, beta member 2 / KCNMB2 / MaxiK channel beta 2 subunit / large conductance calcium-activated potassium channel beta2 subunit


Mass: 5380.064 Da / Num. of mol.: 1 / Fragment: cytoplasmic N-terminus of KCNMB2, residues 1-45 / Source method: obtained synthetically
Details: The 45-residue peptide was synthesized by standard solid-phase synthesis. The sequence occurs naturally in humans.
References: UniProt: Q9Y691

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H-1H NOESY (2D)
121DQF-COSY
1321H-1H NOESY (2D)
NMR detailsText: The structure was determined using standard 2D homonuclear techniques

-
Sample preparation

Details
Solution-IDContentsSolvent system
12mM KCNMB2(residues 1-45), NA; 90% H2O, 10% D2O90% H2O/10% D2O
22mM KCNMB2(residues 1-45), NA; 99.9% D2O99.9% D2O
Sample conditionsIonic strength: 0 / pH: 3.0 / Pressure: ambient / Temperature: 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
AURELIA2.7.5Neidigdata analysis
XEASY1.3.13Bartelsdata analysis
DYANA1.5Mumenthaler, Guentertrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: The structures are based on 728 NOE-derived distance constraints (486 intraresidual, 191 sequential, 51 medium-range), 5 dihedral angle restraints, 11 stereospecific assignments
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations,target function
Conformers calculated total number: 30 / Conformers submitted total number: 24

+
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