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- PDB-7mjq: Vascular KATP channel: Kir6.1 SUR2B quatrefoil-like conformation 2 -

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Basic information

Entry
Database: PDB / ID: 7mjq
TitleVascular KATP channel: Kir6.1 SUR2B quatrefoil-like conformation 2
Components
  • ATP-sensitive inward rectifier potassium channel 8
  • Isoform SUR2B of ATP-binding cassette sub-family C member 9
KeywordsTRANSPORT PROTEIN / KATP / potassium channel / vascular
Function / homology
Function and homology information


cardiac pacemaker cell differentiation / atrioventricular node cell differentiation / vascular process in circulatory system / substrate-dependent cell migration, cell contraction / oxygen metabolic process / reactive oxygen species biosynthetic process / reactive gliosis / response to decreased oxygen levels / ATP sensitive Potassium channels / response to peptide ...cardiac pacemaker cell differentiation / atrioventricular node cell differentiation / vascular process in circulatory system / substrate-dependent cell migration, cell contraction / oxygen metabolic process / reactive oxygen species biosynthetic process / reactive gliosis / response to decreased oxygen levels / ATP sensitive Potassium channels / response to peptide / 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 / sulfonylurea receptor activity / NLRP3 inflammasome complex assembly / ventricular cardiac muscle tissue development / response to hydrogen sulfide / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / response to potassium ion / cardiac conduction / CAMKK-AMPK signaling cascade / circulatory system development / response to oxygen levels / cellular response to potassium ion / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / coronary vasculature development / ATPase-coupled monoatomic cation transmembrane transporter activity / cellular response to chemical stress / vasculature development / regulation of monoatomic ion transmembrane transport / nervous system process / cardiac muscle cell contraction / synaptic assembly at neuromuscular junction / regulation of potassium ion transmembrane transport / inorganic cation transmembrane transport / blood circulation / syntaxin binding / sulfonylurea receptor binding / cellular respiration / response to stress / neuromuscular process / heterocyclic compound binding / cellular response to ATP / Ion homeostasis / establishment of cell polarity / response to ATP / myofibril / action potential / blood vessel development / response to exogenous dsRNA / fat cell differentiation / transmission of nerve impulse / potassium ion import across plasma membrane / p38MAPK cascade / monoatomic cation transmembrane transport / fatty acid oxidation / ATPase-coupled transmembrane transporter activity / potassium channel activity / protein secretion / ABC-type transporter activity / potassium channel regulator activity / heart morphogenesis / fatty acid transport / ATP metabolic process / presynaptic active zone membrane / skeletal muscle tissue development / T-tubule / potassium ion transmembrane transport / negative regulation of blood pressure / response to endoplasmic reticulum stress / regulation of heart rate / sarcomere / cellular response to calcium ion / blood vessel diameter maintenance / acrosomal vesicle / regulation of membrane potential / response to cytokine / kidney development / determination of adult lifespan / response to activity / response to ischemia / mitochondrion organization / calcium ion transmembrane transport / microglial cell activation / response to insulin / potassium ion transport / response to hydrogen peroxide / transmembrane transport / sarcolemma / regulation of blood pressure / response to estrogen / vasodilation / MAPK cascade / cellular response to xenobiotic stimulus / heart development / presynapse / gene expression
Similarity search - Function
Potassium channel, inwardly rectifying, Kir6.1 / ATP-binding cassette subfamily C member 9 / : / 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 ...Potassium channel, inwardly rectifying, Kir6.1 / ATP-binding cassette subfamily C member 9 / : / 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
ADENOSINE-5'-TRIPHOSPHATE / : / ATP-binding cassette sub-family C member 9 / ATP-sensitive inward rectifier potassium channel 8
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsSung, M.W. / Shyng, S.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK066485-13 United States
CitationJournal: 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
DepositionApr 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: ATP-sensitive inward rectifier potassium channel 8
B: ATP-sensitive inward rectifier potassium channel 8
C: ATP-sensitive inward rectifier potassium channel 8
D: ATP-sensitive inward rectifier potassium channel 8
E: Isoform SUR2B of ATP-binding cassette sub-family C member 9
G: Isoform SUR2B of ATP-binding cassette sub-family C member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)544,49614
Polymers541,0736
Non-polymers3,4248
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
ATP-sensitive inward rectifier potassium channel 8 / Inward rectifier K(+) channel Kir6.1 / Potassium channel / inwardly rectifying subfamily J member 8 / uKATP-1


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 Isoform SUR2B of ATP-binding cassette sub-family C member 9 / Sulfonylurea receptor 2


Mass: 174488.562 Da / Num. of mol.: 2
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


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Vascular KATP channel: Kir6.1 SUR2B quatrefoil-like conformation 2
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.889 MDa / Experimental value: YES
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Chlorocebus aethiops (grivet)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
7Cootmodel fitting
9PHENIXmodel refinement
13RELION33D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22038 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6BAA

6baa


Accession code: 6BAA / Source name: PDB / Type: experimental model

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