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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 IONPotassium
  • 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
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 / membrane repolarization during ventricular cardiac muscle cell action potential / ABC-family proteins mediated transport / response to resveratrol / ventricular cardiac muscle tissue development / ATP-activated inward rectifier potassium channel activity ...cardiac pacemaker cell differentiation / atrioventricular node cell differentiation / substrate-dependent cell migration, cell contraction / reactive gliosis / ATP sensitive Potassium channels / membrane repolarization during ventricular cardiac muscle cell action potential / ABC-family proteins mediated transport / response to resveratrol / ventricular cardiac muscle tissue development / ATP-activated inward rectifier potassium channel activity / circulatory system development / glutamate secretion, neurotransmission / inward rectifying potassium channel / NLRP3 inflammasome complex assembly / sulfonylurea receptor activity / 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 / ATPase-coupled monoatomic cation transmembrane transporter activity / coronary vasculature development / vasculature development / cardiac muscle cell contraction / nervous system process / regulation of monoatomic ion transmembrane transport / synaptic assembly at neuromuscular junction / inorganic cation transmembrane transport / syntaxin binding / neuromuscular process / sulfonylurea receptor binding / action potential / Ion homeostasis / response to ATP / establishment of cell polarity / myofibril / response to exogenous dsRNA / heterocyclic compound binding / potassium ion import across plasma membrane / blood vessel development / fat cell differentiation / transmission of nerve impulse / monoatomic cation transmembrane transport / p38MAPK cascade / protein secretion / ATPase-coupled transmembrane transporter activity / potassium channel regulator activity / fatty acid transport / ABC-type transporter activity / heart morphogenesis / presynaptic active zone membrane / potassium ion transmembrane transport / T-tubule / response to endoplasmic reticulum stress / negative regulation of blood pressure / regulation of heart rate / sarcomere / kidney development / response to cytokine / acrosomal vesicle / response to ischemia / determination of adult lifespan / calcium ion transmembrane transport / microglial cell activation / sarcolemma / response to insulin / transmembrane transport / potassium ion transport / regulation of blood pressure / vasodilation / presynapse / gene expression / heart development / fibroblast proliferation / defense response to virus / cell population proliferation / transmembrane transporter binding / response to lipopolysaccharide / adaptive immune response / response to hypoxia / response to xenobiotic stimulus / inflammatory response / glutamatergic synapse / apoptotic process / ATP hydrolysis activity / protein-containing complex / ATP binding / membrane / identical protein binding / plasma membrane
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-
UpdateOct 26, 2022-
Current statusOct 26, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
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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

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
Voxel sizeX=Y=Z: 1.653 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-10.130059 - 13.3662405
Average (Standard dev.)-2.7231193e-11 (±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 IONPotassium
  • 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)
Recombinant expressionOrganism: Chlorocebus aethiops (grivet)
Molecular weightExperimental: 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

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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

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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 / Adenosine triphosphate

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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 / Phosphatidylethanolamine

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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 / POPC

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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 / Glibenclamide

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

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Image processing

Initial angle assignmentType: COMMON LINE
Final angle assignmentType: ANGULAR RECONSTITUTION
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

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Atomic model buiding 1

Initial modelPDB ID:
Output model

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

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