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- PDB-7mit: Vascular KATP channel: Kir6.1 SUR2B propeller-like conformation 1 -

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Basic information

Entry
Database: PDB / ID: 7mit
TitleVascular KATP channel: Kir6.1 SUR2B propeller-like conformation 1
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 / reactive oxygen species biosynthetic process / oxygen metabolic process / synaptic assembly at neuromuscular junction / ATP sensitive Potassium channels / reactive gliosis / response to decreased oxygen levels ...cardiac pacemaker cell differentiation / atrioventricular node cell differentiation / vascular process in circulatory system / substrate-dependent cell migration, cell contraction / reactive oxygen species biosynthetic process / oxygen metabolic process / synaptic assembly at neuromuscular junction / ATP sensitive Potassium channels / reactive gliosis / response to decreased oxygen levels / ABC-family proteins mediated transport / response to peptide / ATP-activated inward rectifier potassium channel activity / potassium channel activator activity / glutamate secretion, neurotransmission / response to resveratrol / inward rectifying potassium channel / membrane repolarization during ventricular cardiac muscle cell action potential / sulfonylurea receptor activity / ventricular cardiac muscle tissue development / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / response to potassium ion / NLRP3 inflammasome complex assembly / CAMKK-AMPK signaling cascade / cardiac conduction / response to oxygen levels / response to hydrogen sulfide / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / regulation of monoatomic ion transmembrane transport / ATPase-coupled monoatomic cation transmembrane transporter activity / cellular respiration / cellular response to chemical stress / coronary vasculature development / vasculature development / cardiac muscle cell contraction / regulation of potassium ion transmembrane transport / circulatory system development / cellular response to potassium ion / heterocyclic compound binding / : / nervous system process / syntaxin binding / blood circulation / Ion homeostasis / sulfonylurea receptor binding / neuromuscular process / response to ATP / response to stress / blood vessel development / establishment of cell polarity / p38MAPK cascade / cellular response to ATP / fat cell differentiation / response to exogenous dsRNA / monoatomic cation transmembrane transport / myofibril / potassium ion import across plasma membrane / fatty acid oxidation / transmission of nerve impulse / action potential / protein secretion / ATPase-coupled transmembrane transporter activity / potassium channel activity / potassium channel regulator activity / ABC-type transporter activity / fatty acid transport / heart morphogenesis / ATP metabolic process / skeletal muscle tissue development / negative regulation of blood pressure / presynaptic active zone membrane / response to cytokine / potassium ion transmembrane transport / T-tubule / acrosomal vesicle / regulation of heart rate / cellular response to calcium ion / response to endoplasmic reticulum stress / blood vessel diameter maintenance / sarcomere / response to ischemia / response to activity / determination of adult lifespan / regulation of membrane potential / mitochondrion organization / kidney development / response to hydrogen peroxide / microglial cell activation / response to insulin / sarcolemma / calcium ion transmembrane transport / potassium ion transport / regulation of blood pressure / transmembrane transport / response to estrogen / vasodilation / cellular response to xenobiotic stimulus / presynapse / MAPK cascade / heart development
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 / Chem-GBM / : / Chem-P5S / Chem-POV / PHOSPHATIDYLETHANOLAMINE / 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: 3.4 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 17, 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 1.2Aug 16, 2023Group: Data collection / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_database_status / pdbx_initial_refinement_model
Item: _pdbx_database_status.pdb_format_compatible
Revision 1.3Nov 6, 2024Group: Data collection / Refinement description / Structure summary
Category: em_3d_fitting_list / em_admin ...em_3d_fitting_list / em_admin / pdbx_entry_details / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)386,90038
Polymers366,5845
Non-polymers20,31633
Water00
1


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

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Components

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Protein , 2 types, 5 molecules ABCDE

#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.: 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

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Sugars , 1 types, 1 molecules

#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.: 1
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 6 types, 32 molecules

#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#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
#6: Chemical
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C42H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#7: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H80NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#8: Chemical
ChemComp-P5S / O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine / phosphatidyl serine


Mass: 792.075 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C42H82NO10P / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-GBM / 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide / Glibenclamide / Glyburide


Mass: 494.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H28ClN3O5S / Feature type: SUBJECT OF INVESTIGATION

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Details

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 propeller-like conformation 1
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
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
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
11RELION3classification
12RELION33D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 139944 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingPDB-ID: 6BAA

6baa


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

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