[English] 日本語
Yorodumi
- EMDB-7338: Cryo-EM structure of human KATP bound to ATP and ADP in quatrefoi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7338
TitleCryo-EM structure of human KATP bound to ATP and ADP in quatrefoil form
Map dataSymmetrized composite map
Sample
  • Complex: Quatrefoil form of human KATP in complex with ATP and ADP
    • Protein or peptide: ATP-sensitive inward rectifier potassium channel 11
    • Protein or peptide: ATP-binding cassette sub-family C member 8
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: POTASSIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsATP-dependent potassium channel Kir6.2 SUR1 ATP ADP / TRANSPORT PROTEIN
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 / potassium ion-transporting ATPase complex / negative regulation of blood-brain barrier permeability / ATP-activated inward rectifier potassium channel activity / glutamate secretion, neurotransmission / response to resveratrol ...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 / potassium ion-transporting ATPase complex / negative regulation of blood-brain barrier permeability / ATP-activated inward rectifier potassium channel activity / glutamate secretion, neurotransmission / response to resveratrol / inward rectifying potassium channel / sulfonylurea receptor activity / ventricular cardiac muscle tissue development / positive regulation of tight junction disassembly / CAMKK-AMPK signaling cascade / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / regulation of monoatomic ion transmembrane transport / positive regulation of potassium ion transport / ATPase-coupled monoatomic cation transmembrane transporter activity / response to pH / negative regulation of low-density lipoprotein particle clearance / nervous system process / : / ankyrin binding / negative regulation of glial cell proliferation / response to zinc ion / neuromuscular process / response to ATP / intracellular glucose homeostasis / potassium ion import across plasma membrane / potassium ion binding / action potential / ATPase-coupled transmembrane transporter activity / voltage-gated potassium channel activity / potassium channel activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / ABC-type transporter activity / cellular response to nutrient levels / Ion homeostasis / potassium ion transmembrane transport / T-tubule / regulation of insulin secretion / negative regulation of angiogenesis / response to ischemia / determination of adult lifespan / regulation of membrane potential / Regulation of insulin secretion / female pregnancy / negative regulation of insulin secretion / response to insulin / sarcolemma / ADP binding / visual learning / ABC-family proteins mediated transport / potassium ion transport / transmembrane transport / memory / glucose metabolic process / positive regulation of tumor necrosis factor production / synaptic vesicle membrane / presynaptic membrane / response to lipopolysaccharide / transmembrane transporter binding / response to hypoxia / response to xenobiotic stimulus / apoptotic process / ATP hydrolysis activity / ATP binding / metal ion binding / membrane / plasma membrane / cytoplasm
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 / : ...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-binding cassette sub-family C member 8 / ATP-sensitive inward rectifier potassium channel 11
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsLee KPK / Chen J
CitationJournal: 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
DepositionJan 10, 2018-
Header (metadata) releaseJan 31, 2018-
Map releaseJan 31, 2018-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.117
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.117
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6c3o
  • Surface level: 0.117
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7338.png

Downloads & links

-
Map

FileDownload / File: emd_7338.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSymmetrized composite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 300 pix.
= 390. Å		1.3 Å/pix.
x 300 pix.
= 390. Å		1.3 Å/pix.
x 300 pix.
= 390. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.117 / Movie #1: 0.117
Minimum - Maximum-1.1543463 - 2.7019334
Average (Standard dev.)0.0003845567 (±0.0195098)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 390.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z390.000390.000390.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-1.1542.7020.000

-
Supplemental data

-
Sample components

-
Entire : Quatrefoil form of human KATP in complex with ATP and ADP

EntireName: Quatrefoil form of human KATP in complex with ATP and ADP
Components
  • Complex: Quatrefoil form of human KATP in complex with ATP and ADP
    • Protein or peptide: ATP-sensitive inward rectifier potassium channel 11
    • Protein or peptide: ATP-binding cassette sub-family C member 8
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: POTASSIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Quatrefoil form of human KATP in complex with ATP and ADP

SupramoleculeName: 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)
Molecular weightTheoretical: 880 kDa/nm

-
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: Homo sapiens (human)
Molecular weightTheoretical: 45.144367 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

UniProtKB: ATP-sensitive inward rectifier potassium channel 11

-
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: Homo sapiens (human)
Molecular weightTheoretical: 177.180219 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

UniProtKB: ATP-binding cassette sub-family C member 8

-
Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 8 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Macromolecule #4: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: K
Molecular weightTheoretical: 39.098 Da

-
Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 4 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

-
Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.45 mg/mL
BufferpH: 8.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.18 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL / In silico model: ab-initio model from cryoSPARC
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 47282
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more