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Yorodumi- EMDB-8470: Cryo-EM structure of the pancreatic ATP-sensitive K+ channel SUR1... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8470 | |||||||||
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Title | Cryo-EM structure of the pancreatic ATP-sensitive K+ channel SUR1/Kir6.2 in the presence of ATP and glibenclamide | |||||||||
Map data | Pancreatic ATP-sensitive K+ channel SUR1/Kir6.2 in the presence of ATP and glibenclamide | |||||||||
Sample |
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Function / homology | Function and homology information Regulation of insulin secretion / ATP sensitive Potassium channels / ABC-family proteins mediated transport / response to resveratrol / ATP-activated inward rectifier potassium channel activity / inward rectifying potassium channel / cell body fiber / sulfonylurea receptor activity / ventricular cardiac muscle tissue development / CAMKK-AMPK signaling cascade ...Regulation of insulin secretion / ATP sensitive Potassium channels / ABC-family proteins mediated transport / response to resveratrol / ATP-activated inward rectifier potassium channel activity / inward rectifying potassium channel / cell body fiber / sulfonylurea receptor activity / ventricular cardiac muscle tissue development / 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 / ankyrin binding / Ion homeostasis / response to ATP / response to testosterone / voltage-gated potassium channel activity / potassium ion import across plasma membrane / action potential / regulation of insulin secretion / potassium channel activity / intercalated disc / axolemma / ABC-type transporter activity / negative regulation of insulin secretion / potassium ion transmembrane transport / T-tubule / heat shock protein binding / positive regulation of protein localization to plasma membrane / potassium ion transport / acrosomal vesicle / regulation of membrane potential / response to ischemia / determination of adult lifespan / cellular response to glucose stimulus / sarcolemma / cellular response to nicotine / glucose metabolic process / nuclear envelope / response to estradiol / cellular response to tumor necrosis factor / presynaptic membrane / transmembrane transporter binding / endosome / response to hypoxia / response to xenobiotic stimulus / neuronal cell body / glutamatergic synapse / apoptotic process / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) / Cricetus cricetus (black-bellied hamster) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.3 Å | |||||||||
Authors | Martin GM / Yoshioka C / Chen JZ / Shyng SL | |||||||||
Funding support | United States, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8470.map.gz | 70.6 MB | EMDB map data format | |
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Header (meta data) | emd-8470-v30.xml emd-8470.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8470_fsc.xml | 12.6 KB | Display | FSC data file |
Images | emd_8470.png | 286.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8470 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8470 | HTTPS FTP |
-Validation report
Summary document | emd_8470_validation.pdf.gz | 546.6 KB | Display | EMDB validaton report |
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Full document | emd_8470_full_validation.pdf.gz | 546.1 KB | Display | |
Data in XML | emd_8470_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | emd_8470_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8470 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8470 | HTTPS FTP |
-Related structure data
Related structure data | 5twvMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8470.map.gz / Format: CCP4 / Size: 76.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Pancreatic ATP-sensitive K+ channel SUR1/Kir6.2 in the presence of ATP and glibenclamide | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : ATP-sensitive K+ channel complex SUR1/Kir6.2
Entire | Name: ATP-sensitive K+ channel complex SUR1/Kir6.2 |
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Components |
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-Supramolecule #1: ATP-sensitive K+ channel complex SUR1/Kir6.2
Supramolecule | Name: ATP-sensitive K+ channel complex SUR1/Kir6.2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
-Supramolecule #2: SUR1
Supramolecule | Name: SUR1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Cricetus cricetus (black-bellied hamster) |
Recombinant expression | Organism: Rattus norvegicus (Norway rat) / Recombinant cell: INS-1 / Recombinant plasmid: pShuttle-TetR:pAdEasy |
-Supramolecule #3: Kir6.2
Supramolecule | Name: Kir6.2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Recombinant expression | Organism: Rattus norvegicus (Norway rat) / Recombinant cell: INS-1 / Recombinant plasmid: pShuttle-CMV:pAdEasy |
-Macromolecule #1: ATP-sensitive inward rectifier potassium channel 11
Macromolecule | Name: ATP-sensitive inward rectifier potassium channel 11 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 43.645719 KDa |
Recombinant expression | Organism: Rattus norvegicus (Norway rat) |
Sequence | String: 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 |
-Macromolecule #2: ATP-binding cassette sub-family C member 8
Macromolecule | Name: ATP-binding cassette sub-family C member 8 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Cricetus cricetus (black-bellied hamster) |
Molecular weight | Theoretical: 178.330516 KDa |
Recombinant expression | Organism: Rattus norvegicus (Norway rat) |
Sequence | String: 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 |
-Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |