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Yorodumi- PDB-5ywd: Structure of pancreatic ATP-sensitive potassium channel bound wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ywd | ||||||||||||||||||
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Title | Structure of pancreatic ATP-sensitive potassium channel bound with Mg-ADP (focused refinement of SUR1 ABC transporter module at 4.22A) | ||||||||||||||||||
Components | ATP-binding cassette sub-family C member 8 isoform X2 | ||||||||||||||||||
Keywords | MEMBRANE PROTEIN / KATP / channel / glibenclamide / sulfonylurea | ||||||||||||||||||
Function / homology | Function and homology information glutamate secretion, neurotransmission / inward rectifying potassium channel / sulfonylurea receptor activity / ATPase-coupled monoatomic cation transmembrane transporter activity / inorganic cation transmembrane transport / neuromuscular process / potassium channel activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of insulin secretion / ABC-type transporter activity ...glutamate secretion, neurotransmission / inward rectifying potassium channel / sulfonylurea receptor activity / ATPase-coupled monoatomic cation transmembrane transporter activity / inorganic cation transmembrane transport / neuromuscular process / potassium channel activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of insulin secretion / ABC-type transporter activity / ADP binding / presynapse / transmembrane transporter binding / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||||||||||||||
Biological species | Mesocricetus auratus (golden hamster) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||||||||||||||
Authors | Chen, L. / Wu, J.X. | ||||||||||||||||||
Funding support | China, 5items
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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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5ywd.cif.gz | 235.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ywd.ent.gz | 180.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ywd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ywd_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5ywd_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5ywd_validation.xml.gz | 48.2 KB | Display | |
Data in CIF | 5ywd_validation.cif.gz | 71.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/5ywd ftp://data.pdbj.org/pub/pdb/validation_reports/yw/5ywd | HTTPS FTP |
-Related structure data
Related structure data | 6853MC 6831C 6832C 6833C 6847C 6848C 6849C 6850C 6851C 6852C 5ykeC 5ykfC 5ykgC 5yw7C 5yw8C 5yw9C 5ywaC 5ywbC 5ywcC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 177295.516 Da / Num. of mol.: 1 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 | ||
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#2: Chemical | #3: Chemical | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: KATP / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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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 |
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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 |
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CTF correction | Type: NONE |
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 721684 / Symmetry type: POINT |