[English] 日本語
Yorodumi- PDB-5yw8: Structure of pancreatic ATP-sensitive potassium channel bound wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yw8 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of pancreatic ATP-sensitive potassium channel bound with ATPgammaS (all particles at 4.4A) | ||||||||||||||||||
Components |
| ||||||||||||||||||
Keywords | MEMBRANE PROTEIN / KATP / channel / glibenclamide / sulfonylurea | ||||||||||||||||||
Function / homology | Function and homology information ATP sensitive Potassium channels / response to resveratrol / ATP-activated inward rectifier potassium channel activity / glutamate secretion, neurotransmission / inward rectifying potassium channel / cell body fiber / Regulation of insulin secretion / sulfonylurea receptor activity / ventricular cardiac muscle tissue development / CAMKK-AMPK signaling cascade ...ATP sensitive Potassium channels / response to resveratrol / ATP-activated inward rectifier potassium channel activity / glutamate secretion, neurotransmission / inward rectifying potassium channel / cell body fiber / Regulation of insulin secretion / sulfonylurea receptor activity / ventricular cardiac muscle tissue development / CAMKK-AMPK signaling cascade / ABC-family proteins mediated transport / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / response to stress / 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 / neuromuscular process / ankyrin binding / response to ATP / response to testosterone / potassium ion import across plasma membrane / action potential / positive regulation of insulin secretion involved in cellular response to glucose stimulus / potassium ion binding / potassium channel activity / intercalated disc / axolemma / ABC-type transporter activity / cellular response to nutrient levels / negative regulation of insulin secretion / T-tubule / heat shock protein binding / positive regulation of protein localization to plasma membrane / potassium ion transport / acrosomal vesicle / response to ischemia / determination of adult lifespan / cellular response to glucose stimulus / sarcolemma / ADP binding / cellular response to nicotine / glucose metabolic process / nuclear envelope / response to estradiol / cellular response to tumor necrosis factor / presynapse / presynaptic membrane / transmembrane transporter binding / endosome / response to hypoxia / response to xenobiotic stimulus / neuronal cell body / glutamatergic synapse / apoptotic process / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Mus musculus (house mouse) Mesocricetus auratus (golden hamster) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å | ||||||||||||||||||
Authors | Chen, L. / Wu, J.X. | ||||||||||||||||||
Funding support | China, 5items
| ||||||||||||||||||
Citation | Journal: Protein Cell / Year: 2018 Title: Ligand binding and conformational changes of SUR1 subunit in pancreatic ATP-sensitive potassium channels. Authors: Jing-Xiang Wu / Dian Ding / Mengmeng Wang / Yunlu Kang / Xin Zeng / Lei Chen / Abstract: ATP-sensitive potassium channels (K) are energy sensors on the plasma membrane. By sensing the intracellular ADP/ATP ratio of β-cells, pancreatic K channels control insulin release and regulate ...ATP-sensitive potassium channels (K) are energy sensors on the plasma membrane. By sensing the intracellular ADP/ATP ratio of β-cells, pancreatic K channels control insulin release and regulate metabolism at the whole body level. They are implicated in many metabolic disorders and diseases and are therefore important drug targets. Here, we present three structures of pancreatic K channels solved by cryo-electron microscopy (cryo-EM), at resolutions ranging from 4.1 to 4.5 Å. These structures depict the binding site of the antidiabetic drug glibenclamide, indicate how Kir6.2 (inward-rectifying potassium channel 6.2) N-terminus participates in the coupling between the peripheral SUR1 (sulfonylurea receptor 1) subunit and the central Kir6.2 channel, reveal the binding mode of activating nucleotides, and suggest the mechanism of how Mg-ADP binding on nucleotide binding domains (NBDs) drives a conformational change of the SUR1 subunit. | ||||||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5yw8.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5yw8.ent.gz | 925.7 KB | Display | PDB format |
PDBx/mmJSON format | 5yw8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yw8_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5yw8_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 5yw8_validation.xml.gz | 189.4 KB | Display | |
Data in CIF | 5yw8_validation.cif.gz | 278.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/5yw8 ftp://data.pdbj.org/pub/pdb/validation_reports/yw/5yw8 | HTTPS FTP |
-Related structure data
Related structure data | 6848MC 6831C 6832C 6833C 6847C 6849C 6850C 6851C 6852C 6853C 5ykeC 5ykfC 5ykgC 5yw7C 5yw9C 5ywaC 5ywbC 5ywcC 5ywdC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 43615.734 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kcnj11 / Production host: Homo sapiens (human) / References: UniProt: Q61743 #2: Protein | Mass: 177295.516 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mesocricetus auratus (golden hamster) / Gene: Abcc8 / Production host: Homo sapiens (human) / References: UniProt: A0A1U7R319 #3: Chemical | ChemComp-AGS / |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: KATP / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
EM software | Name: RELION / Version: 2 / Category: 3D reconstruction |
---|---|
CTF correction | Type: NONE |
3D reconstruction | Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28499 / Symmetry type: POINT |