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Yorodumi- PDB-6c3p: Cryo-EM structure of human KATP bound to ATP and ADP in propeller form -
+Open data
-Basic information
Entry | Database: PDB / ID: 6c3p | ||||||
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Title | Cryo-EM structure of human KATP bound to ATP and ADP in propeller form | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / ATP-dependent potassium channel Kir6.2 SUR1 ATP ADP | ||||||
Function / homology | Function and homology information Defective ABCC9 causes CMD10, ATFB12 and Cantu syndrome / negative regulation of neuroblast migration / positive regulation of uterine smooth muscle relaxation / ATP sensitive Potassium channels / Defective ABCC8 can cause hypo- and hyper-glycemias / positive regulation of tight junction disassembly / potassium ion-transporting ATPase complex / negative regulation of blood-brain barrier permeability / ATP-activated inward rectifier potassium channel activity / glutamate secretion, neurotransmission ...Defective ABCC9 causes CMD10, ATFB12 and Cantu syndrome / negative regulation of neuroblast migration / positive regulation of uterine smooth muscle relaxation / ATP sensitive Potassium channels / Defective ABCC8 can cause hypo- and hyper-glycemias / positive regulation of tight junction disassembly / potassium ion-transporting ATPase complex / negative regulation of blood-brain barrier permeability / ATP-activated inward rectifier potassium channel activity / glutamate secretion, neurotransmission / inward rectifying potassium channel / negative regulation of low-density lipoprotein particle clearance / sulfonylurea receptor activity / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / positive regulation of potassium ion transport / inward rectifier potassium channel activity / ATPase-coupled monoatomic cation transmembrane transporter activity / nervous system process / regulation of monoatomic ion transmembrane transport / response to pH / inorganic cation transmembrane transport / neuromuscular process / ankyrin binding / negative regulation of glial cell proliferation / response to ATP / : / response to zinc ion / intracellular glucose homeostasis / voltage-gated potassium channel activity / potassium ion import across plasma membrane / positive regulation of insulin secretion involved in cellular response to glucose stimulus / potassium ion binding / regulation of insulin secretion / potassium channel activity / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / negative regulation of insulin secretion / negative regulation of angiogenesis / Ion homeostasis / potassium ion transmembrane transport / T-tubule / potassium ion transport / regulation of membrane potential / Regulation of insulin secretion / female pregnancy / response to insulin / visual learning / ABC-family proteins mediated transport / sarcolemma / transmembrane transport / memory / ADP binding / synaptic vesicle membrane / glucose metabolic process / positive regulation of tumor necrosis factor production / transmembrane transporter binding / response to lipopolysaccharide / response to xenobiotic stimulus / ATP hydrolysis activity / ATP binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.6 Å | ||||||
Authors | Lee, K.P.K. / Chen, J. / MacKinnon, R. | ||||||
Citation | Journal: Elife / Year: 2017 Title: Molecular structure of human KATP in complex with ATP and ADP. Authors: Kenneth Pak Kin Lee / Jue Chen / Roderick MacKinnon / Abstract: In many excitable cells, KATP channels respond to intracellular adenosine nucleotides: ATP inhibits while ADP activates. We present two structures of the human pancreatic KATP channel, containing the ...In many excitable cells, KATP channels respond to intracellular adenosine nucleotides: ATP inhibits while ADP activates. We present two structures of the human pancreatic KATP channel, containing the ABC transporter SUR1 and the inward-rectifier K channel Kir6.2, in the presence of Mg and nucleotides. These structures, referred to as quatrefoil and propeller forms, were determined by single-particle cryo-EM at 3.9 Å and 5.6 Å, respectively. In both forms, ATP occupies the inhibitory site in Kir6.2. The nucleotide-binding domains of SUR1 are dimerized with Mg-ATP in the degenerate site and Mg-ADP in the consensus site. A lasso extension forms an interface between SUR1 and Kir6.2 adjacent to the ATP site in the propeller form and is disrupted in the quatrefoil form. These structures support the role of SUR1 as an ADP sensor and highlight the lasso extension as a key regulatory element in ADP's ability to override ATP inhibition. | ||||||
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 | 6c3p.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6c3p.ent.gz | 932.3 KB | Display | PDB format |
PDBx/mmJSON format | 6c3p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6c3p_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6c3p_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6c3p_validation.xml.gz | 186.9 KB | Display | |
Data in CIF | 6c3p_validation.cif.gz | 276.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/6c3p ftp://data.pdbj.org/pub/pdb/validation_reports/c3/6c3p | HTTPS FTP |
-Related structure data
Related structure data | 7339MC 7338C 6c3oC 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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-Components
#1: Protein | Mass: 45144.367 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KCNJ11 / Production host: Homo sapiens (human) / References: UniProt: Q14654 #2: Protein | Mass: 177180.219 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ABCC8, HRINS, SUR, SUR1 / Production host: Homo sapiens (human) / References: UniProt: Q09428 #3: Chemical | ChemComp-ATP / #4: Chemical | ChemComp-ADP / #5: Chemical | ChemComp-MG / |
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-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: Quatrefoil form of human KATP in complex with ATP and ADP Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 0.88 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8.5 |
Specimen | Conc.: 0.45 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K |
-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: 1.18 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47282 / Symmetry type: POINT |