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- EMDB-8470: Cryo-EM structure of the pancreatic ATP-sensitive K+ channel SUR1... -

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Basic information

Entry
Database: EMDB / ID: EMD-8470
TitleCryo-EM structure of the pancreatic ATP-sensitive K+ channel SUR1/Kir6.2 in the presence of ATP and glibenclamide
Map dataPancreatic ATP-sensitive K+ channel SUR1/Kir6.2 in the presence of ATP and glibenclamide
Sample
  • Complex: ATP-sensitive K+ channel complex SUR1/Kir6.2
    • Complex: SUR1ABCC8
      • Protein or peptide: ATP-binding cassette sub-family C member 8
    • Complex: Kir6.2
      • Protein or peptide: ATP-sensitive inward rectifier potassium channel 11
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Function / homology
Function and homology information


Regulation of insulin secretion / ATP sensitive Potassium channels / ABC-family proteins mediated transport / response to resveratrol / ventricular cardiac muscle tissue development / ATP-activated inward rectifier potassium channel activity / cell body fiber / inward rectifying potassium channel / sulfonylurea receptor activity / CAMKK-AMPK signaling cascade ...Regulation of insulin secretion / ATP sensitive Potassium channels / ABC-family proteins mediated transport / response to resveratrol / ventricular cardiac muscle tissue development / ATP-activated inward rectifier potassium channel activity / cell body fiber / inward rectifying potassium channel / sulfonylurea receptor activity / CAMKK-AMPK signaling cascade / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / inward rectifier potassium channel activity / ATPase-coupled monoatomic cation transmembrane transporter activity / nervous system process / regulation of monoatomic ion transmembrane transport / inorganic cation transmembrane transport / action potential / ankyrin binding / Ion homeostasis / response to ATP / response to testosterone / potassium ion import across plasma membrane / voltage-gated potassium channel activity / potassium channel activity / regulation of insulin secretion / axolemma / intercalated disc / negative regulation of insulin secretion / ABC-type transporter activity / potassium ion transmembrane transport / T-tubule / heat shock protein binding / regulation of membrane potential / acrosomal vesicle / response to ischemia / determination of adult lifespan / positive regulation of protein localization to plasma membrane / cellular response to glucose stimulus / sarcolemma / potassium ion transport / cellular response to nicotine / glucose metabolic process / response to estradiol / presynaptic membrane / nuclear envelope / cellular response to tumor necrosis factor / transmembrane transporter binding / response to hypoxia / endosome / response to xenobiotic stimulus / neuronal cell body / glutamatergic synapse / apoptotic process / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Potassium channel, inwardly rectifying, Kir6.2 / ATP-binding cassette subfamily C member 8 / 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 ...Potassium channel, inwardly rectifying, Kir6.2 / ATP-binding cassette subfamily C member 8 / 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-sensitive inward rectifier potassium channel 11 / ATP-binding cassette sub-family C member 8
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Cricetus cricetus (black-bellied hamster)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsMartin GM / Yoshioka C / Chen JZ / Shyng SL
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK066485 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)F31DK105300 United States
CitationJournal: Elife / Year: 2017
Title: Cryo-EM structure of the ATP-sensitive potassium channel illuminates mechanisms of assembly and gating.
Authors: Gregory M Martin / Craig Yoshioka / Emily A Rex / Jonathan F Fay / Qing Xie / Matthew R Whorton / James Z Chen / Show-Ling Shyng /
Abstract: K channels are metabolic sensors that couple cell energetics to membrane excitability. In pancreatic β-cells, channels formed by SUR1 and Kir6.2 regulate insulin secretion and are the targets of ...K channels are metabolic sensors that couple cell energetics to membrane excitability. In pancreatic β-cells, channels formed by SUR1 and Kir6.2 regulate insulin secretion and are the targets of antidiabetic sulfonylureas. Here, we used cryo-EM to elucidate structural basis of channel assembly and gating. The structure, determined in the presence of ATP and the sulfonylurea glibenclamide, at ~6 Å resolution reveals a closed Kir6.2 tetrameric core with four peripheral SUR1s each anchored to a Kir6.2 by its N-terminal transmembrane domain (TMD0). Intricate interactions between TMD0, the loop following TMD0, and Kir6.2 near the proposed PIP binding site, and where ATP density is observed, suggest SUR1 may contribute to ATP and PIP binding to enhance Kir6.2 sensitivity to both. The SUR1-ABC core is found in an unusual inward-facing conformation whereby the two nucleotide binding domains are misaligned along a two-fold symmetry axis, revealing a possible mechanism by which glibenclamide inhibits channel activity.
History
DepositionNov 14, 2016-
Header (metadata) releaseNov 23, 2016-
Map releaseJan 25, 2017-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5twv
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8470.map.gz / Format: CCP4 / Size: 76.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPancreatic ATP-sensitive K+ channel SUR1/Kir6.2 in the presence of ATP and glibenclamide
Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy EMDB: 0.027736 / Movie #1: 0.03
Minimum - Maximum-0.03780731 - 0.094522804
Average (Standard dev.)0.0027735932 (±0.010320818)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions272272272
Spacing272272272
CellA=B=C: 233.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z272272272
origin x/y/z0.0000.0000.000
length x/y/z233.920233.920233.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS272272272
D min/max/mean-0.0380.0950.003

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Supplemental data

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Sample components

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Entire : ATP-sensitive K+ channel complex SUR1/Kir6.2

EntireName: ATP-sensitive K+ channel complex SUR1/Kir6.2
Components
  • Complex: ATP-sensitive K+ channel complex SUR1/Kir6.2
    • Complex: SUR1ABCC8
      • Protein or peptide: ATP-binding cassette sub-family C member 8
    • Complex: Kir6.2
      • Protein or peptide: ATP-sensitive inward rectifier potassium channel 11
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: ATP-sensitive K+ channel complex SUR1/Kir6.2

SupramoleculeName: ATP-sensitive K+ channel complex SUR1/Kir6.2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Supramolecule #2: SUR1

SupramoleculeName: SUR1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Cricetus cricetus (black-bellied hamster)
Recombinant expressionOrganism: Rattus norvegicus (Norway rat) / Recombinant cell: INS-1 / Recombinant plasmid: pShuttle-TetR:pAdEasy

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Supramolecule #3: Kir6.2

SupramoleculeName: Kir6.2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Rattus norvegicus (Norway rat) / Recombinant cell: INS-1 / Recombinant plasmid: pShuttle-CMV:pAdEasy

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Macromolecule #1: ATP-sensitive inward rectifier potassium channel 11

MacromoleculeName: ATP-sensitive inward rectifier potassium channel 11 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 43.645719 KDa
Recombinant expressionOrganism: Rattus norvegicus (Norway rat)
SequenceString: MLSRKGIIPE EYVLTRLAED PTEPRYRTRE RRARFVSKKG NCNVAHKNIR EQGRFLQDVF TTLVDLKWPH TLLIFTMSFL CSWLLFAMV WWLIAFAHGD LAPGEGTNVP CVTSIHSFSS AFLFSIEVQV TIGFGGRMVT EECPLAILIL IVQNIVGLMI N AIMLGCIF ...String:
MLSRKGIIPE EYVLTRLAED PTEPRYRTRE RRARFVSKKG NCNVAHKNIR EQGRFLQDVF TTLVDLKWPH TLLIFTMSFL CSWLLFAMV WWLIAFAHGD LAPGEGTNVP CVTSIHSFSS AFLFSIEVQV TIGFGGRMVT EECPLAILIL IVQNIVGLMI N AIMLGCIF MKTAQAHRRA ETLIFSKHAV ITPRHGRLCF MLRVGDLRKS MIISATIHMQ VVRKTTSPEG EVVPLHQVDI PM ENGVGGN SIFLVAPLII YHVIDSNSPL YDLAPSDLHH HQDLEIIVIL EGVVETTGIT TQARTSYLAD EILWGQRFVP IVA EEDGRY SVDYSKFGNT VKVPTPLCTA RQLDEDRSLL DALTLASSRG PLRKRSVAVA KAKPKFSISP DSLS

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Macromolecule #2: ATP-binding cassette sub-family C member 8

MacromoleculeName: ATP-binding cassette sub-family C member 8 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Cricetus cricetus (black-bellied hamster)
Molecular weightTheoretical: 178.330516 KDa
Recombinant expressionOrganism: Rattus norvegicus (Norway rat)
SequenceString: DYKDDDDKMP LAFCGTENHS AAYRVDQGVL NNGCFVDALN VVPHVFLLFI TFPILFIGWG SQSSKVHIHH STWLHFPGHN LRWILTFIL LFVLVCEIAE GILSDGVTES RHLHLYMPAG MAFMAAITSV VYYHNIETSN FPKLLIALLI YWTLAFITKT I KFVKFYDH ...String:
DYKDDDDKMP LAFCGTENHS AAYRVDQGVL NNGCFVDALN VVPHVFLLFI TFPILFIGWG SQSSKVHIHH STWLHFPGHN LRWILTFIL LFVLVCEIAE GILSDGVTES RHLHLYMPAG MAFMAAITSV VYYHNIETSN FPKLLIALLI YWTLAFITKT I KFVKFYDH AIGFSQLRFC LTGLLVILYG MLLLVEVNVI RVRRYIFFKT PREVKPPEDL QDLGVRFLQP FVNLLSKGTY WW MNAFIKT AHKKPIDLRA IAKLPIAMRA LTNYQRLCVA FDAQARKDTQ SPQGARAIWR ALCHAFGRRL ILSSTFRILA DLL GFAGPL CIFGIVDHLG KENHVFQPKT QFLGVYFVSS QEFLGNAYVL AVLLFLALLL QRTFLQASYY VAIETGINLR GAIQ TKIYN KIMHMSTSNL SMGEMTAGQI CNLVAIDTNQ LMWFFFLCPN LWTMPVQIIV GVILLYYILG VSALIGAAVI ILLAP VQYF VATKLSQAQR TTLEHSNERL KQTNEMLRGM KLLKLYAWES IFCSRVEVTR RKEMTSLRAF AVYTSISIFM NTAIPI AAV LITFVGHVSF FKESDLSPSV AFASLSLFHI LVTPLFLLSS VVRSTVKALV SVQKLSEFLS SAEIREEQCA PREPAPQ GQ AGKYQAVPLK VVNRKRPARE EVRDLLGPLQ RLAPSMDGDA DNFCVQIIGG FFTWTPDGIP TLSNITIRIP RGQLTMIV G QVGCGKSSLL LATLGEMQKV SGAVFWNSNL PDSEGEDPSS PERETAAGSD IRSRGPVAYA SQKPWLLNAT VEENITFES PFNKQRYKMV IEACSLQPDI DILPHGDQTQ IGERGINLSG GQRQRISVAR ALYQQTNVVF LDDPFSALDV HLSDHLMQAG ILELLRDDK RTVVLVTHKL QYLPHADWII AMKDGTIQRE GTLKDFQRSE CQLFEHWKTL MNRQDQELEK ETVMERKASE P SQGLPRAM SSRDGLLLDE EEEEEEAAES EEDDNLSSVL HQRAKIPWRA CTKYLSSAGI LLLSLLVFSQ LLKHMVLVAI DY WLAKWTD SALVLSPAAR NCSLSQECDL DQSVYAMVFT LLCSLGIVLC LVTSVTVEWT GLKVAKRLHR SLLNRIILAP MRF FETTPL GSILNRFSSD CNTIDQHIPS TLECLSRSTL LCVSALTVIS YVTPVFLVAL LPLAVVCYFI QKYFRVASRD LQQL DDTTQ LPLVSHFAET VEGLTTIRAF RYEARFQQKL LEYTDSNNIA SLFLTAANRW LEVCMEYIGA CVVLIAAATS ISNSL HREL SAGLVGLGLT YALMVSNYLN WMVRNLADME IQLGAVKRIH ALLKTEAESY EGLLAPSLIP KNWPDQGKIQ IQNLSV RYD SSLKPVLKHV NTLISPGQKI GICGRTGSGK SSFSLAFFRM VDMFEGRIII DGIDIAKLPL HTLRSRLSII LQDPVLF SG TIRFNLDPEK KCSDSTLWEA LEIAQLKLVV KALPGGLDAI ITEGGENFSQ GQRQLFCLAR AFVRKTSIFI MDEATASI D MATENILQKV VMTAFADRTV VTIAHRVHTI LSADLVMVLK RGAILEFDKP ETLLSQKDSV FASFVRADK

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / 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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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 20000
FSC plot (resolution estimation)

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