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Yorodumi- PDB-7mjp: Vascular KATP channel: Kir6.1 SUR2B propeller-like conformation 2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mjp | ||||||
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Title | Vascular KATP channel: Kir6.1 SUR2B propeller-like conformation 2 | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / KATP / potassium channel / vascular | ||||||
Function / homology | Function and homology information cardiac pacemaker cell differentiation / atrioventricular node cell differentiation / substrate-dependent cell migration, cell contraction / reactive gliosis / ATP sensitive Potassium channels / ABC-family proteins mediated transport / response to resveratrol / ATP-activated inward rectifier potassium channel activity / membrane repolarization during ventricular cardiac muscle cell action potential / glutamate secretion, neurotransmission ...cardiac pacemaker cell differentiation / atrioventricular node cell differentiation / substrate-dependent cell migration, cell contraction / reactive gliosis / ATP sensitive Potassium channels / ABC-family proteins mediated transport / response to resveratrol / ATP-activated inward rectifier potassium channel activity / membrane repolarization during ventricular cardiac muscle cell action potential / glutamate secretion, neurotransmission / inward rectifying potassium channel / NLRP3 inflammasome complex assembly / sulfonylurea receptor activity / ventricular cardiac muscle tissue development / circulatory system development / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / CAMKK-AMPK signaling cascade / cardiac conduction / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / coronary vasculature development / ATPase-coupled monoatomic cation transmembrane transporter activity / vasculature development / nervous system process / cardiac muscle cell contraction / response to stress / synaptic assembly at neuromuscular junction / inorganic cation transmembrane transport / regulation of monoatomic ion transmembrane transport / syntaxin binding / sulfonylurea receptor binding / neuromuscular process / Ion homeostasis / response to ATP / establishment of cell polarity / myofibril / heterocyclic compound binding / response to exogenous dsRNA / blood vessel development / fat cell differentiation / transmission of nerve impulse / p38MAPK cascade / potassium ion import across plasma membrane / action potential / monoatomic cation transmembrane transport / ATPase-coupled transmembrane transporter activity / protein secretion / potassium channel regulator activity / ABC-type transporter activity / heart morphogenesis / fatty acid transport / presynaptic active zone membrane / potassium ion transmembrane transport / T-tubule / negative regulation of blood pressure / response to endoplasmic reticulum stress / sarcomere / regulation of heart rate / acrosomal vesicle / response to cytokine / kidney development / response to ischemia / determination of adult lifespan / calcium ion transmembrane transport / microglial cell activation / response to insulin / potassium ion transport / sarcolemma / transmembrane transport / regulation of blood pressure / vasodilation / presynapse / heart development / gene expression / fibroblast proliferation / defense response to virus / transmembrane transporter binding / adaptive immune response / response to lipopolysaccharide / cell population proliferation / response to hypoxia / inflammatory response / response to xenobiotic stimulus / glutamatergic synapse / apoptotic process / ATP hydrolysis activity / protein-containing complex / ATP binding / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||
Authors | Sung, M.W. / Shyng, S.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Vascular K channel structural dynamics reveal regulatory mechanism by Mg-nucleotides. Authors: Min Woo Sung / Zhongying Yang / Camden M Driggers / Bruce L Patton / Barmak Mostofian / John D Russo / Daniel M Zuckerman / Show-Ling Shyng / Abstract: Vascular tone is dependent on smooth muscle K channels comprising pore-forming Kir6.1 and regulatory SUR2B subunits, in which mutations cause Cantú syndrome. Unique among K isoforms, they lack ...Vascular tone is dependent on smooth muscle K channels comprising pore-forming Kir6.1 and regulatory SUR2B subunits, in which mutations cause Cantú syndrome. Unique among K isoforms, they lack spontaneous activity and require Mg-nucleotides for activation. Structural mechanisms underlying these properties are unknown. Here, we determined cryogenic electron microscopy structures of vascular K channels bound to inhibitory ATP and glibenclamide, which differ informatively from similarly determined pancreatic K channel isoform (Kir6.2/SUR1). Unlike SUR1, SUR2B subunits adopt distinct rotational "propeller" and "quatrefoil" geometries surrounding their Kir6.1 core. The glutamate/aspartate-rich linker connecting the two halves of the SUR-ABC core is observed in a quatrefoil-like conformation. Molecular dynamics simulations reveal MgADP-dependent dynamic tripartite interactions between this linker, SUR2B, and Kir6.1. The structures captured implicate a progression of intermediate states between MgADP-free inactivated, and MgADP-bound activated conformations wherein the glutamate/aspartate-rich linker participates as mobile autoinhibitory domain, suggesting a conformational pathway toward K channel activation. | ||||||
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 | 7mjp.cif.gz | 406.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mjp.ent.gz | 280.2 KB | Display | PDB format |
PDBx/mmJSON format | 7mjp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mjp_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7mjp_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7mjp_validation.xml.gz | 60.3 KB | Display | |
Data in CIF | 7mjp_validation.cif.gz | 98.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/7mjp ftp://data.pdbj.org/pub/pdb/validation_reports/mj/7mjp | HTTPS FTP |
-Related structure data
Related structure data | 23881MC 7mitC 7mjoC 7mjqC 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: 48023.871 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcnj8 / Production host: Chlorocebus aethiops (grivet) / References: UniProt: Q63664 #2: Protein | | Mass: 174488.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Abcc9, Sur2 / Production host: Chlorocebus aethiops (grivet) / References: UniProt: Q63563 #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Chemical | ChemComp-ATP / #5: Chemical | ChemComp-GBM / | Has ligand of interest | Y | |
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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: Vascular KATP channel: Kir6.1 SUR2B propeller-like conformation 2 Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 0.889 MDa / Experimental value: YES |
Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Source (recombinant) | Organism: Chlorocebus aethiops (grivet) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70830 / Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | PDB-ID: 6BAA Accession code: 6BAA / Source name: PDB / Type: experimental model |