[English] 日本語
Yorodumi- EMDB-7338: Cryo-EM structure of human KATP bound to ATP and ADP in quatrefoi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7338 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of human KATP bound to ATP and ADP in quatrefoil form | |||||||||
Map data | Symmetrized composite map | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information Defective ABCC9 causes CMD10, ATFB12 and Cantu syndrome / negative regulation of neuroblast migration / positive regulation of uterine smooth muscle relaxation / ATP sensitive Potassium channels / Defective ABCC8 can cause hypo- and hyper-glycemias / positive regulation of tight junction disassembly / potassium ion-transporting ATPase complex / negative regulation of blood-brain barrier permeability / ATP-activated inward rectifier potassium channel activity / glutamate secretion, neurotransmission ...Defective ABCC9 causes CMD10, ATFB12 and Cantu syndrome / negative regulation of neuroblast migration / positive regulation of uterine smooth muscle relaxation / ATP sensitive Potassium channels / Defective ABCC8 can cause hypo- and hyper-glycemias / positive regulation of tight junction disassembly / potassium ion-transporting ATPase complex / negative regulation of blood-brain barrier permeability / ATP-activated inward rectifier potassium channel activity / glutamate secretion, neurotransmission / inward rectifying potassium channel / negative regulation of low-density lipoprotein particle clearance / sulfonylurea receptor activity / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / positive regulation of potassium ion transport / inward rectifier potassium channel activity / ATPase-coupled monoatomic cation transmembrane transporter activity / nervous system process / regulation of monoatomic ion transmembrane transport / response to pH / inorganic cation transmembrane transport / neuromuscular process / ankyrin binding / negative regulation of glial cell proliferation / response to ATP / : / response to zinc ion / intracellular glucose homeostasis / voltage-gated potassium channel activity / potassium ion import across plasma membrane / positive regulation of insulin secretion involved in cellular response to glucose stimulus / potassium ion binding / regulation of insulin secretion / potassium channel activity / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / negative regulation of insulin secretion / negative regulation of angiogenesis / Ion homeostasis / potassium ion transmembrane transport / T-tubule / potassium ion transport / regulation of membrane potential / Regulation of insulin secretion / female pregnancy / response to insulin / visual learning / ABC-family proteins mediated transport / sarcolemma / transmembrane transport / memory / ADP binding / synaptic vesicle membrane / glucose metabolic process / positive regulation of tumor necrosis factor production / transmembrane transporter binding / response to lipopolysaccharide / response to xenobiotic stimulus / ATP hydrolysis activity / ATP binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Lee KPK / Chen J / MacKinnon R | |||||||||
Citation | Journal: Elife / Year: 2017 Title: Molecular structure of human KATP in complex with ATP and ADP. Authors: Kenneth Pak Kin Lee / Jue Chen / Roderick MacKinnon / Abstract: In many excitable cells, KATP channels respond to intracellular adenosine nucleotides: ATP inhibits while ADP activates. We present two structures of the human pancreatic KATP channel, containing the ...In many excitable cells, KATP channels respond to intracellular adenosine nucleotides: ATP inhibits while ADP activates. We present two structures of the human pancreatic KATP channel, containing the ABC transporter SUR1 and the inward-rectifier K channel Kir6.2, in the presence of Mg and nucleotides. These structures, referred to as quatrefoil and propeller forms, were determined by single-particle cryo-EM at 3.9 Å and 5.6 Å, respectively. In both forms, ATP occupies the inhibitory site in Kir6.2. The nucleotide-binding domains of SUR1 are dimerized with Mg-ATP in the degenerate site and Mg-ADP in the consensus site. A lasso extension forms an interface between SUR1 and Kir6.2 adjacent to the ATP site in the propeller form and is disrupted in the quatrefoil form. These structures support the role of SUR1 as an ADP sensor and highlight the lasso extension as a key regulatory element in ADP's ability to override ATP inhibition. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7338.map.gz | 95.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-7338-v30.xml emd-7338.xml | 15 KB 15 KB | Display Display | EMDB header |
Images | emd_7338.png | 56.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7338 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7338 | HTTPS FTP |
-Validation report
Summary document | emd_7338_validation.pdf.gz | 343.8 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_7338_full_validation.pdf.gz | 343.3 KB | Display | |
Data in XML | emd_7338_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | emd_7338_validation.cif.gz | 6.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7338 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7338 | HTTPS FTP |
-Related structure data
Related structure data | 6c3oMC 7339C 6c3pC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_7338.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Symmetrized composite map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Quatrefoil form of human KATP in complex with ATP and ADP
Entire | Name: Quatrefoil form of human KATP in complex with ATP and ADP |
---|---|
Components |
|
-Supramolecule #1: Quatrefoil form of human KATP in complex with ATP and ADP
Supramolecule | Name: Quatrefoil form of human KATP in complex with ATP and ADP type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 880 kDa/nm |
-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 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 45.144367 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: SASASAMLSR KGIIPEEYVL TRLAEDPAEP RYRARQRRAR FVSKKGNCNV AHKNIREQGR FLQDVFTTLV DLKWPHTLLI FTMSFLCSW LLFAMAWWLI AFAHGDLAPS EGTAEPCVTS IHSFSSAFLF SIEVQVTIGF GGRMVTEECP LAILILIVQN I VGLMINAI ...String: SASASAMLSR KGIIPEEYVL TRLAEDPAEP RYRARQRRAR FVSKKGNCNV AHKNIREQGR FLQDVFTTLV DLKWPHTLLI FTMSFLCSW LLFAMAWWLI AFAHGDLAPS EGTAEPCVTS IHSFSSAFLF SIEVQVTIGF GGRMVTEECP LAILILIVQN I VGLMINAI MLGCIFMKTA QAHRRAETLI FSKHAVIALR HGRLCFMLRV GDLRKSMIIS ATIHMQVVRK TTSPEGEVVP LH QVDIPME NGVGGNSIFL VAPLIIYHVI DANSPLYDLA PSDLHHHQDL EIIVILEGVV ETTGITTQAR TSYLADEILW GQR FVPIVA EEDGRYSVDY SKFGNTIKVP TPLCTARQLD EDHSLLEALT LASARGPLRK RSVPMAKAKP KFSISPDSLS SNSL EVLFQ G |
-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 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 177.180219 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MPLAFCGSEN HSAAYRVDQG VLNNGCFVDA LNVVPHVFLL FITFPILFIG WGSQSSKVHI HHSTWLHFPG HNLRWILTFM LLFVLVCEI AEGILSDGVT ESHHLHLYMP AGMAFMAAVT SVVYYHNIET SNFPKLLIAL LVYWTLAFIT KTIKFVKFLD H AIGFSQLR ...String: MPLAFCGSEN HSAAYRVDQG VLNNGCFVDA LNVVPHVFLL FITFPILFIG WGSQSSKVHI HHSTWLHFPG HNLRWILTFM LLFVLVCEI AEGILSDGVT ESHHLHLYMP AGMAFMAAVT SVVYYHNIET SNFPKLLIAL LVYWTLAFIT KTIKFVKFLD H AIGFSQLR FCLTGLLVIL YGMLLLVEVN VIRVRRYIFF KTPREVKPPE DLQDLGVRFL QPFVNLLSKG TYWWMNAFIK TA HKKPIDL RAIGKLPIAM RALTNYQRLC EAFDAQVRKD IQGTQGARAI WQALSHAFGR RLVLSSTFRI LADLLGFAGP LCI FGIVDH LGKENDVFQP KTQFLGVYFV SSQEFLANAY VLAVLLFLAL LLQRTFLQAS YYVAIETGIN LRGAIQTKIY NKIM HLSTS NLSMGEMTAG QICNLVAIDT NQLMWFFFLC PNLWAMPVQI IVGVILLYYI LGVSALIGAA VIILLAPVQY FVATK LSQA QRSTLEYSNE RLKQTNEMLR GIKLLKLYAW ENIFRTRVET TRRKEMTSLR AFAIYTSISI FMNTAIPIAA VLITFV GHV SFFKEADFSP SVAFASLSLF HILVTPLFLL SSVVRSTVKA LVSVQKLSEF LSSAEIREEQ CAPHEPTPQG PASKYQA VP LRVVNRKRPA REDCRGLTGP LQSLVPSADG DADNCCVQIM GGYFTWTPDG IPTLSNITIR IPRGQLTMIV GQVGCGKS S LLLAALGEMQ KVSGAVFWSS LPDSEIGEDP SPERETATDL DIRKRGPVAY ASQKPWLLNA TVEENIIFES PFNKQRYKM VIEACSLQPD IDILPHGDQT QIGERGINLS GGQRQRISVA RALYQHANVV FLDDPFSALD IHLSDHLMQA GILELLRDDK RTVVLVTHK LQYLPHADWI IAMKDGTIQR EGTLKDFQRS ECQLFEHWKT LMNRQDQELE KETVTERKAT EPPQGLSRAM S SRDGLLQD EEEEEEEAAE SEEDDNLSSM LHQRAEIPWR ACAKYLSSAG ILLLSLLVFS QLLKHMVLVA IDYWLAKWTD SA LTLTPAA RNCSLSQECT LDQTVYAMVF TVLCSLGIVL CLVTSVTVEW TGLKVAKRLH RSLLNRIILA PMRFFETTPL GSI LNRFSS DCNTIDQHIP STLECLSRST LLCVSALAVI SYVTPVFLVA LLPLAIVCYF IQKYFRVASR DLQQLDDTTQ LPLL SHFAE TVEGLTTIRA FRYEARFQQK LLEYTDSNNI ASLFLTAANR WLEVRMEYIG ACVVLIAAVT SISNSLHREL SAGLV GLGL TYALMVSNYL NWMVRNLADM ELQLGAVKRI HGLLKTEAES YEGLLAPSLI PKNWPDQGKI QIQNLSVRYD SSLKPV LKH VNALIAPGQK IGICGRTGSG KSSFSLAFFR MVDTFEGHII IDGIDIAKLP LHTLRSRLSI ILQDPVLFSG TIRFNLD PE RKCSDSTLWE ALEIAQLKLV VKALPGGLDA IITEGGENFS QGQRQLFCLA RAFVRKTSIF IMDEATASID MATENILQ K VVMTAFADRT VVTIAHRVHT ILSADLVIVL KRGAILEFDK PEKLLSRKDS VFASFVRADK |
-Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 8 / Formula: ATP |
---|---|
Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #4: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: K |
---|---|
Molecular weight | Theoretical: 39.098 Da |
-Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 4 / Formula: ADP |
---|---|
Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 8 / Formula: MG |
---|---|
Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.45 mg/mL |
---|---|
Buffer | pH: 8.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.18 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |