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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 data
SampleATP-sensitive K+ channel complex SUR1/Kir6.2
  • SUR1ABCC8
  • Kir6.2
  • ATP-sensitive inward rectifier potassium channel 11
  • ATP-binding cassette sub-family C member 8
  • ligand
Function / homology
Function and homology information


inward rectifying potassium channel / ATP-activated inward rectifier potassium channel activity / sulfonylurea receptor activity / cell body fiber / inorganic cation transmembrane transport / ATPase-coupled cation transmembrane transporter activity / inward rectifier potassium channel activity / positive regulation of cation channel activity / potassium ion import across plasma membrane / ankyrin binding ...inward rectifying potassium channel / ATP-activated inward rectifier potassium channel activity / sulfonylurea receptor activity / cell body fiber / inorganic cation transmembrane transport / ATPase-coupled cation transmembrane transporter activity / inward rectifier potassium channel activity / positive regulation of cation channel activity / potassium ion import across plasma membrane / ankyrin binding / nervous system process / response to ATP / axolemma / potassium channel activity / intercalated disc / response to testosterone / potassium ion transmembrane transport / ATPase-coupled transmembrane transporter activity / voltage-gated potassium channel activity / regulation of ion transmembrane transport / negative regulation of insulin secretion / regulation of insulin secretion / T-tubule / acrosomal vesicle / heat shock protein binding / response to ischemia / potassium ion transport / regulation of membrane potential / cellular response to glucose stimulus / sarcolemma / positive regulation of protein localization to plasma membrane / nuclear envelope / cellular response to nicotine / glucose metabolic process / cellular response to tumor necrosis factor / myelin sheath / response to estradiol / ion channel binding / protein C-terminus binding / endosome / ATPase activity / response to drug / intracellular membrane-bounded organelle / neuronal cell body / endoplasmic reticulum / mitochondrion / integral component of membrane / ATP binding / plasma membrane / cytosol
Sulphonylurea receptor / ATP-binding cassette subfamily C member 8 / Potassium channel, inwardly rectifying, Kir6.2 / Inward rectifier potassium channel, C-terminal / Potassium channel, inwardly rectifying, transmembrane domain / ABC transporter type 1, transmembrane domain superfamily / P-loop containing nucleoside triphosphate hydrolase / ABC transporter, conserved site / Potassium channel, inwardly rectifying, Kir / Immunoglobulin E-set ...Sulphonylurea receptor / ATP-binding cassette subfamily C member 8 / Potassium channel, inwardly rectifying, Kir6.2 / Inward rectifier potassium channel, C-terminal / Potassium channel, inwardly rectifying, transmembrane domain / ABC transporter type 1, transmembrane domain superfamily / P-loop containing nucleoside triphosphate hydrolase / ABC transporter, conserved site / Potassium channel, inwardly rectifying, Kir / Immunoglobulin E-set / Potassium channel, inwardly rectifying, Kir, cytoplasmic / ABC transporter type 1, transmembrane domain / AAA+ ATPase domain / ABC transporter-like
ATP-sensitive inward rectifier potassium channel 11 / ATP-binding cassette sub-family C member 8
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.
Validation ReportPDB-ID: 5twv

SummaryFull reportAbout validation report
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
  • Download
  • 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)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 272 pix.
= 233.92 Å
0.86 Å/pix.
x 272 pix.
= 233.92 Å
0.86 Å/pix.
x 272 pix.
= 233.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

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 / Number of components: 6

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Component #1: protein, ATP-sensitive K+ channel complex SUR1/Kir6.2

ProteinName: ATP-sensitive K+ channel complex SUR1/Kir6.2 / Recombinant expression: No
SourceSpecies: Rattus norvegicus (Norway rat)

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Component #2: protein, SUR1

ProteinName: SUR1ABCC8 / Recombinant expression: No
SourceSpecies: Cricetus cricetus (black-bellied hamster)
Source (engineered)Expression System: Rattus norvegicus (Norway rat) / Vector: pShuttle-TetR:pAdEasy / Cell of expression system: INS-1

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Component #3: protein, Kir6.2

ProteinName: Kir6.2 / Recombinant expression: No
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Rattus norvegicus (Norway rat) / Vector: pShuttle-CMV:pAdEasy / Cell of expression system: INS-1

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Component #4: protein, ATP-sensitive inward rectifier potassium channel 11

ProteinName: ATP-sensitive inward rectifier potassium channel 11 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 43.645719 kDa
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Rattus norvegicus (Norway rat)

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Component #5: protein, ATP-binding cassette sub-family C member 8

ProteinName: ATP-binding cassette sub-family C member 8 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 178.330516 kDa
SourceSpecies: Cricetus cricetus (black-bellied hamster)
Source (engineered)Expression System: Rattus norvegicus (Norway rat)

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Component #6: ligand, ADENOSINE-5'-TRIPHOSPHATE

LigandName: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 81000.0 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 3000.0 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 20000
3D reconstructionSoftware: RELION / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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