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- EMDB-23880: Vascular KATP channel: Kir6.1 SUR2B quatrefoil-like conformation 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-23880
TitleVascular KATP channel: Kir6.1 SUR2B quatrefoil-like conformation 1
Map datasharpened-Q1-S4-Final2021
Sample
  • Complex: Vascular KATP channel: Kir6.1 SUR2B quatrefoil-like conformation 2
    • Protein or peptide: ATP-sensitive inward rectifier potassium channel 8
    • Protein or peptide: Isoform SUR2B of ATP-binding cassette sub-family C member 9
  • Ligand: POTASSIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide
KeywordsKATP / potassium channel / vascular / TRANSPORT PROTEIN
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 / response to decreased oxygen levels / reactive gliosis / 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 / response to decreased oxygen levels / reactive gliosis / 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 / 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 / response to hydrogen sulfide / 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 / cellular response to ATP / Ion homeostasis / establishment of cell polarity / response to ATP / myofibril / heterocyclic compound binding / 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 / action potential / fatty acid oxidation / potassium channel activity / ATPase-coupled transmembrane transporter 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 / regulation of heart rate / response to endoplasmic reticulum stress / sarcomere / cellular response to calcium ion / blood vessel diameter maintenance / acrosomal vesicle / regulation of membrane potential / response to cytokine / kidney development / response to activity / response to ischemia / mitochondrion organization / determination of adult lifespan / calcium ion transmembrane transport / microglial cell activation / response to insulin / potassium ion transport / response to hydrogen peroxide / sarcolemma / transmembrane transport / regulation of blood pressure / response to estrogen / vasodilation / MAPK cascade / cellular response to xenobiotic stimulus / presynapse / heart development / 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
ATP-binding cassette sub-family C member 9 / ATP-sensitive inward rectifier potassium channel 8
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsSung MW / Shyng SL
Funding support United States, 1 items
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, 2021-
Header (metadata) releaseOct 13, 2021-
Map releaseOct 13, 2021-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
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  • Surface view with fitted model
  • Atomic models: PDB-7mjo
  • Surface level: 1
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23880.png

Downloads & links

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Map

FileDownload / File: emd_23880.map.gz / Format: CCP4 / Size: 2.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened-Q1-S4-Final2021
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.65 Å/pix.
x 94 pix.
= 155.382 Å		1.65 Å/pix.
x 98 pix.
= 161.994 Å		1.65 Å/pix.
x 74 pix.
= 122.322 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.653 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-10.130058999999999 - 13.3662405
Average (Standard dev.)-0.000000000027231 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin908478
Dimensions987494
Spacing749894
CellA: 122.322 Å / B: 161.994 Å / C: 155.382 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.6531.6531.653
M x/y/z749894
origin x/y/z0.0000.0000.000
length x/y/z122.322161.994155.382
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ440440440
MAP C/R/S123
start NC/NR/NS849078
NC/NR/NS749894
D min/max/mean-10.13013.366-0.000

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Supplemental data

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Sample components

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Entire : Vascular KATP channel: Kir6.1 SUR2B quatrefoil-like conformation 2

EntireName: Vascular KATP channel: Kir6.1 SUR2B quatrefoil-like conformation 2
Components
  • Complex: Vascular KATP channel: Kir6.1 SUR2B quatrefoil-like conformation 2
    • Protein or peptide: ATP-sensitive inward rectifier potassium channel 8
    • Protein or peptide: Isoform SUR2B of ATP-binding cassette sub-family C member 9
  • Ligand: POTASSIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide

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Supramolecule #1: Vascular KATP channel: Kir6.1 SUR2B quatrefoil-like conformation 2

SupramoleculeName: Vascular KATP channel: Kir6.1 SUR2B quatrefoil-like conformation 2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 889 KDa

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Macromolecule #1: ATP-sensitive inward rectifier potassium channel 8

MacromoleculeName: ATP-sensitive inward rectifier potassium channel 8 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 48.023871 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet)
SequenceString: MLARKSIIPE EYVLARIAAE NLRKPRIRDR LPKARFIAKS GACNLAHKNI REQGRFLQDI FTTLVDLKWR HTLVIFTMSF LCSWLLFAI MWWLVAFAHG DIYAYMEKGI TEKSGLESAV CVTNVRSFTS AFLFSIEVQV TIGFGGRMMT EECPLAITVL I LQNIVGLI ...String:
MLARKSIIPE EYVLARIAAE NLRKPRIRDR LPKARFIAKS GACNLAHKNI REQGRFLQDI FTTLVDLKWR HTLVIFTMSF LCSWLLFAI MWWLVAFAHG DIYAYMEKGI TEKSGLESAV CVTNVRSFTS AFLFSIEVQV TIGFGGRMMT EECPLAITVL I LQNIVGLI INAVMLGCIF MKTAQAHRRA ETLIFSRHAV IAVRNGKLCF MFRVGDLRKS MIISASVRIQ VVKKTTTPEG EV VPIHQQD IPVDNPIESN NIFLVAPLII CHVIDKRSPL YDISATDLVN QDLEVIVILE GVVETTGITT QARTSYIAEE IQW GHRFVS IVTEEEGVYS VDYSKFGNTV RVAAPRCSAR ELDEKPSILI QTLQKSELSH QNSLRKRNSM RRNNSMRRSN SIRR NNSSL MVPKVQFMTP EGNQCPSES

UniProtKB: ATP-sensitive inward rectifier potassium channel 8

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Macromolecule #2: Isoform SUR2B of ATP-binding cassette sub-family C member 9

MacromoleculeName: Isoform SUR2B of ATP-binding cassette sub-family C member 9
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 174.488562 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet)
SequenceString: MSLSFCGNNI SSYNIYHGVL QNPCFVDALN LVPHVFLLFI TFPILFIGWG SQSSKVQIHH NTWLHFPGHN LRWILTFALL FVHVCEIAE GIVSDSQRAS RHLHLFMPAV MGFVATTTSI VYYHNIETSN FPKLLLALFL YWVMAFITKT IKLVKYWQLG W GMSDLRFC ...String:
MSLSFCGNNI SSYNIYHGVL QNPCFVDALN LVPHVFLLFI TFPILFIGWG SQSSKVQIHH NTWLHFPGHN LRWILTFALL FVHVCEIAE GIVSDSQRAS RHLHLFMPAV MGFVATTTSI VYYHNIETSN FPKLLLALFL YWVMAFITKT IKLVKYWQLG W GMSDLRFC ITGVMVILNG LLMAVEINVI RVRRYVFFMN PQKVKPPEDL QDLGVRFLQP FVNLLSKATY WWMNTLIISA HR KPIDLKA IGKLPIAMRA VTNYVCLKEA YEEQKKKAAD HPNRTPSIWL AMYRAFGRPI LLSSTFRYLA DLLGFAGPLC ISG IVQRVN EPKNNTTRFS ETLSSKEFLE NAHVLAVLLF LALILQRTFL QASYYVTIET GINLRGALLA MIYNKILRLS TSNL SMGEM TLGQINNLVA IETNQLMWFL FLCPNLWAMP VQIIMGVILL YNLLGSSALV GAAVIVLLAP IQYFIATKLA EAQKS TLDY STERLKKTNE ILKGIKLLKL YAWEHIFCKS VEETRMKELS SLKTFALYTS LSIFMNAAIP IAAVLATFVT HAYASG NNL KPAEAFASLS LFHILVTPLF LLSTVVRFAV KAIISVQKLN EFLLSDEIGE DSWRTGEGTL PFESCKKHTG VQSKPIN RK QPGRYHLDNY EQARRLRPAE TEDVAIKVTN GYFSWGSGLA TLSNIDIRIP TGQLTMIVGQ VGCGKSSLLL AILGEMQT L EGKVYWNNVN ESEPSFEATR SRSRYSVAYA AQKPWLLNAT VEENITFGSS FNRQRYKAVT DACSLQPDID LLPFGDQTE IGERGINLSG GQRQRICVAR ALYQNTNIVF LDDPFSALDI HLSDHLMQEG ILKFLQDDKR TVVLVTHKLQ YLTHADWIIA MKDGSVLRE GTLKDIQTKD VELYEHWKTL MNRQDQELEK DMEADQTTLE RKTLRRAMYS REAKAQMEDE DEEEEEEEDE D DNMSTVMR LRTKMPWKTC WWYLTSGGFF LLFLMIFSKL LKHSVIVAID YWLATWTSEY SINDPGKADQ TFYVAGFSIL CG AGIFLCL VTSLTVEWMG LTAAKNLHHN LLNKIILGPI RFFDTTPLGL ILNRFSADTN IIDQHIPPTL ESLTRSTLLC LSA IGMISY ATPVFLIALA PLGVAFYFIQ KYFRVASKDL QELDDSTQLP LLCHFSETAE GLTTIRAFRH ETRFKQRMLE LTDT NNIAY LFLSAANRWL EVRTDYLGAC IVLTASIASI SGSSNSGLVG LGLLYALTIT NYLNWVVRNL ADLEVQMGAV KKVNS FLTM ESENYEGTMD PSQVPEHWPQ EGEIKIHDLC VRYENNLKPV LKHVKAYIKP GQKVGICGRT GSGKSSLSLA FFRMVD IFD GKIVIDGIDI SKLPLHTLRS RLSIILQDPI LFSGSIRFNL DPECKCTDDR LWEALEIAQL KNMVKSLPGG LDATVTE GG ENFSVGQRQL FCLARAFVRK SSILIMDEAT ASIDMATENI LQKVVMTAFA DRTVVTIAHR VHTILTADLV IVMKRGNI L EYDTPESLLA QEDGVFASFV RADM

UniProtKB: ATP-binding cassette sub-family C member 9

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Macromolecule #4: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 5 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #6: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 6 / Number of copies: 10 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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Macromolecule #7: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 7 / Number of copies: 3 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #8: 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-...

MacromoleculeName: 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide
type: ligand / ID: 8 / Number of copies: 1 / Formula: GBM
Molecular weightTheoretical: 494.004 Da
Chemical component information

ChemComp-GBM:
5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide / medication*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/1 / Support film - Material: GRAPHENE OXIDE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 71880
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

Initial modelPDB ID:

6baa


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

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

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