[English] 日本語
Yorodumi
- EMDB-3265: Single particle analysis of ATP-sensitive potassium channel -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3265
TitleSingle particle analysis of ATP-sensitive potassium channel
Map dataHeterooctamer complex of hamster SUR1 and mouse Kir6.2
Sample
  • Sample: ATP-sensitive potassium channel complex consisting of hamster SUR1 and mouse Kir6.2
  • Protein or peptide: ATP-binding cassette sub-family C member 8
  • Protein or peptide: ATP-sensitive inward rectifier potassium channel 11
Keywordspotassium channel / ABC transporter / ATP-sensitive potassium channel
Function / homology
Function and homology information


ATP sensitive Potassium channels / response to resveratrol / ventricular cardiac muscle tissue development / ATP-activated inward rectifier potassium channel activity / cell body fiber / inward rectifying potassium channel / Regulation of insulin secretion / sulfonylurea receptor activity / CAMKK-AMPK signaling cascade / ABC-family proteins mediated transport ...ATP sensitive Potassium channels / response to resveratrol / ventricular cardiac muscle tissue development / ATP-activated inward rectifier potassium channel activity / cell body fiber / inward rectifying potassium channel / Regulation of insulin secretion / sulfonylurea receptor activity / CAMKK-AMPK signaling cascade / ABC-family proteins mediated transport / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / Ion homeostasis / inward rectifier potassium channel activity / ATPase-coupled monoatomic cation transmembrane transporter activity / nervous system process / regulation of monoatomic ion transmembrane transport / inorganic cation transmembrane transport / action potential / ankyrin binding / response to ATP / response to testosterone / potassium ion import across plasma membrane / voltage-gated potassium channel activity / potassium ion binding / potassium channel activity / regulation of insulin secretion / axolemma / intercalated disc / negative regulation of insulin secretion / ABC-type transporter activity / potassium ion transmembrane transport / T-tubule / heat shock protein binding / regulation of membrane potential / acrosomal vesicle / response to ischemia / determination of adult lifespan / cellular response to glucose stimulus / positive regulation of protein localization to plasma membrane / sarcolemma / potassium ion transport / cellular response to nicotine / glucose metabolic process / response to estradiol / presynaptic membrane / nuclear envelope / cellular response to tumor necrosis factor / transmembrane transporter binding / response to hypoxia / endosome / response to xenobiotic stimulus / neuronal cell body / glutamatergic synapse / apoptotic process / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Potassium channel, inwardly rectifying, Kir6.2 / ATP-binding cassette subfamily C member 8 / Sulphonylurea receptor / Potassium channel, inwardly rectifying, transmembrane domain / Inward rectifier potassium channel transmembrane domain / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain / ABC transporter transmembrane region ...Potassium channel, inwardly rectifying, Kir6.2 / ATP-binding cassette subfamily C member 8 / Sulphonylurea receptor / Potassium channel, inwardly rectifying, transmembrane domain / Inward rectifier potassium channel transmembrane domain / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Immunoglobulin E-set / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-binding cassette sub-family C member 8 / ATP-sensitive inward rectifier potassium channel 11
Similarity search - Component
Biological speciesCricetus cricetus (black-bellied hamster) / Mus musculus (house mouse)
Methodsingle particle reconstruction / negative staining / Resolution: 18.0 Å
AuthorsKimura Y / Kanno R / Matsuo M / Kato H / Mitsuoka K / Kazumitsu U
CitationJournal: The Journal of Biological Chemistry
Title: Nucleotide-dependent conformational change of the ATP-sensitive potassium channel
Authors: Kimura Y / Kanno R / Matsuo M / Kato H / Mitsuoka K / Kazumitsu U
History
DepositionNov 27, 2015-
Header (metadata) releaseJan 27, 2016-
Map releaseMay 31, 2017-
UpdateMay 31, 2017-
Current statusMay 31, 2017Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.23
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.23
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3265.png

Downloads & links

-
Map

FileDownload / File: emd_3265.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHeterooctamer complex of hamster SUR1 and mouse Kir6.2
Voxel sizeX=Y=Z: 3.6 Å
Density
Contour LevelBy AUTHOR: 0.23 / Movie #1: 0.23
Minimum - Maximum-0.31650114 - 0.79723728
Average (Standard dev.)0.01637996 (±0.08898084)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-49-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 360.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.63.63.6
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z360.000360.000360.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-50-49-50
NC/NR/NS100100100
D min/max/mean-0.3170.7970.016

-
Supplemental data

-
Sample components

-
Entire : ATP-sensitive potassium channel complex consisting of hamster SUR...

EntireName: ATP-sensitive potassium channel complex consisting of hamster SUR1 and mouse Kir6.2
Components
  • Sample: ATP-sensitive potassium channel complex consisting of hamster SUR1 and mouse Kir6.2
  • Protein or peptide: ATP-binding cassette sub-family C member 8
  • Protein or peptide: ATP-sensitive inward rectifier potassium channel 11

-
Supramolecule #1000: ATP-sensitive potassium channel complex consisting of hamster SUR...

SupramoleculeName: ATP-sensitive potassium channel complex consisting of hamster SUR1 and mouse Kir6.2
type: sample / ID: 1000
Oligomeric state: Four SUR1 and four Kir6.2 forms heterooctamer
Number unique components: 2
Molecular weightTheoretical: 880 KDa

-
Macromolecule #1: ATP-binding cassette sub-family C member 8

MacromoleculeName: ATP-binding cassette sub-family C member 8 / type: protein_or_peptide / ID: 1 / Name.synonym: ABCC8, SUR1 / Number of copies: 4 / Recombinant expression: Yes
Source (natural)Organism: Cricetus cricetus (black-bellied hamster) / synonym: Black-bellied hamster
Molecular weightTheoretical: 180 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant strain: human / Recombinant cell: FreeStyle 293F / Recombinant plasmid: pCDNA3.1
SequenceUniProtKB: ATP-binding cassette sub-family C member 8

-
Macromolecule #2: ATP-sensitive inward rectifier potassium channel 11

MacromoleculeName: ATP-sensitive inward rectifier potassium channel 11 / type: protein_or_peptide / ID: 2 / Name.synonym: KCNJ11, Kir6.2 / Number of copies: 4 / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: Mouse
Molecular weightTheoretical: 44 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant strain: human / Recombinant cell: FreeStyle 293F / Recombinant plasmid: pCDNA3.1
SequenceUniProtKB: ATP-sensitive inward rectifier potassium channel 11

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.2
Details: 50 mM HEPES-Na, 50 mM NaCl, 50 mM KCl, 5% glycerol, 1 mM 2-mercaptoethanol, 0.05% C12E8
StainingType: NEGATIVE
Details: Purified protein was stained with 2% uranyl acetate for 10 seconds on a carbon-coated copper grid
GridDetails: 400 mesh copper grid with thin carbon support, glow discharged
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeJEOL 1010
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsCalibrated magnification: 38400 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 30000
Sample stageSpecimen holder model: JEOL
DateJun 9, 2009
Image recordingCategory: CCD / Film or detector model: OTHER / Number real images: 34 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0

-
Image processing

Final two d classificationNumber classes: 82
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: OTHER / Software - Name: IMAGIC / Number images used: 12117
DetailsThe particles were selected using an automatic selection program.

+
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