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- EMDB-32025: Structure of SUR2B in complex with MgATP/ADP and P1075 -

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Basic information

Entry
Database: EMDB / ID: EMD-32025
TitleStructure of SUR2B in complex with MgATP/ADP and P1075
Map datasharpened map of SUR2B in complex with Mg-nucleotides and P1075
Sample
  • Complex: ATP-binding cassette sub-family C member 9, isoform B
    • Protein or peptide: Isoform SUR2B of ATP-binding cassette sub-family C member 9
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 1-cyano-2-(2-methylbutan-2-yl)-3-pyridin-3-yl-guanidine
KeywordsSUR2B / ABC transporter / P1075 / MEMBRANE PROTEIN
Function / homology
Function and homology information


vascular process in circulatory system / substrate-dependent cell migration, cell contraction / oxygen metabolic process / reactive oxygen species biosynthetic process / response to decreased oxygen levels / ATP sensitive Potassium channels / response to peptide / ABC-family proteins mediated transport / inward rectifying potassium channel / sulfonylurea receptor activity ...vascular process in circulatory system / substrate-dependent cell migration, cell contraction / oxygen metabolic process / reactive oxygen species biosynthetic process / response to decreased oxygen levels / ATP sensitive Potassium channels / response to peptide / ABC-family proteins mediated transport / inward rectifying potassium channel / sulfonylurea receptor activity / response to hydrogen sulfide / response to potassium ion / cardiac conduction / circulatory system development / response to oxygen levels / cellular response to potassium ion / coronary vasculature development / ATPase-coupled monoatomic cation transmembrane transporter activity / cellular response to chemical stress / cardiac muscle cell contraction / regulation of potassium ion transmembrane transport / inorganic cation transmembrane transport / blood circulation / syntaxin binding / cellular respiration / response to stress / heterocyclic compound binding / cellular response to ATP / Ion homeostasis / response to ATP / action potential / blood vessel development / potassium ion import across plasma membrane / monoatomic cation transmembrane transport / fatty acid oxidation / ATPase-coupled transmembrane transporter activity / potassium channel activity / ABC-type transporter activity / potassium channel regulator activity / heart morphogenesis / ATP metabolic process / skeletal muscle tissue development / T-tubule / potassium ion transmembrane transport / negative regulation of blood pressure / sarcomere / cellular response to calcium ion / blood vessel diameter maintenance / acrosomal vesicle / regulation of membrane potential / response to activity / mitochondrion organization / 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 / gene expression / fibroblast proliferation / defense response to virus / transmembrane transporter binding / response to hypoxia / response to xenobiotic stimulus / protein-containing complex binding / negative regulation of apoptotic process / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / mitochondrion / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
ATP-binding cassette subfamily C member 9 / : / Sulphonylurea receptor / : / 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. ...ATP-binding cassette subfamily C member 9 / : / Sulphonylurea receptor / : / 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. / 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
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsChen L / Ding D
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91957201 China
National Natural Science Foundation of China (NSFC)31870833 China
National Natural Science Foundation of China (NSFC)31821091 China
CitationJournal: Nat Commun / Year: 2022
Title: Structural identification of vasodilator binding sites on the SUR2 subunit.
Authors: Dian Ding / Jing-Xiang Wu / Xinli Duan / Songling Ma / Lipeng Lai / Lei Chen /
Abstract: ATP-sensitive potassium channels (K), composed of Kir6 and SUR subunits, convert the metabolic status of the cell into electrical signals. Pharmacological activation of SUR2- containing K channels by ...ATP-sensitive potassium channels (K), composed of Kir6 and SUR subunits, convert the metabolic status of the cell into electrical signals. Pharmacological activation of SUR2- containing K channels by class of small molecule drugs known as K openers leads to hyperpolarization of excitable cells and to vasodilation. Thus, K openers could be used to treat cardiovascular diseases. However, where these vasodilators bind to K and how they activate the channel remains elusive. Here, we present cryo-EM structures of SUR2A and SUR2B subunits in complex with Mg-nucleotides and P1075 or levcromakalim, two chemically distinct K openers that are specific to SUR2. Both P1075 and levcromakalim bind to a common site in the transmembrane domain (TMD) of the SUR2 subunit, which is between TMD1 and TMD2 and is embraced by TM10, TM11, TM12, TM14, and TM17. These K openers synergize with Mg-nucleotides to stabilize SUR2 in the NBD-dimerized occluded state to activate the channel.
History
DepositionOct 5, 2021-
Header (metadata) releaseMay 18, 2022-
Map releaseMay 18, 2022-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32025.png

Downloads & links

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Map

FileDownload / File: emd_32025.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map of SUR2B in complex with Mg-nucleotides and P1075
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 200 pix.
= 262.8 Å		1.31 Å/pix.
x 200 pix.
= 262.8 Å		1.31 Å/pix.
x 200 pix.
= 262.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.314 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.31
Minimum - Maximum-3.8198216 - 6.1706376
Average (Standard dev.)0.009187066 (±0.15390383)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 262.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-A map of SUR2B in complex with Mg-nucleotides and P1075

Fileemd_32025_half_map_1.map
AnnotationHalf-A map of SUR2B in complex with Mg-nucleotides and P1075
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-B map of SUR2B in complex with Mg-nucleotides and P1075

Fileemd_32025_half_map_2.map
AnnotationHalf-B map of SUR2B in complex with Mg-nucleotides and P1075
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ATP-binding cassette sub-family C member 9, isoform B

EntireName: ATP-binding cassette sub-family C member 9, isoform B
Components
  • Complex: ATP-binding cassette sub-family C member 9, isoform B
    • Protein or peptide: Isoform SUR2B of ATP-binding cassette sub-family C member 9
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 1-cyano-2-(2-methylbutan-2-yl)-3-pyridin-3-yl-guanidine

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Supramolecule #1: ATP-binding cassette sub-family C member 9, isoform B

SupramoleculeName: ATP-binding cassette sub-family C member 9, isoform B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 174 kDa/nm

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Macromolecule #1: 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: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 174.488562 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / 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: 1-cyano-2-(2-methylbutan-2-yl)-3-pyridin-3-yl-guanidine

MacromoleculeName: 1-cyano-2-(2-methylbutan-2-yl)-3-pyridin-3-yl-guanidine
type: ligand / ID: 6 / Number of copies: 1 / Formula: ESV
Molecular weightTheoretical: 231.297 Da
Chemical component information

ChemComp-ESV:
1-cyano-2-(2-methylbutan-2-yl)-3-pyridin-3-yl-guanidine

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1.0) / Number images used: 124387
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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