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- EMDB-24839: Human KATP channel in open conformation, focused on Kir (C166S G3... -

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Basic information

Entry
Database: EMDB / ID: EMD-24839
TitleHuman KATP channel in open conformation, focused on Kir (C166S G334D double mutant) and SUR TMD0
Map datamap focus-refined on Kir and SUR TMD0 after sharpening (B-factor: 77.1)
Sample
  • Complex: Human KATP channel composed of Kir6.2 (C166S G334D) and SUR1
    • Protein or peptide: ATP-sensitive inward rectifier potassium channel 11
  • Ligand: POTASSIUM ION
Keywordsion channel / KATP / ATP-sensitive potassium channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


response to resveratrol / ATP-activated inward rectifier potassium channel activity / inward rectifying potassium channel / ventricular cardiac muscle tissue development / cell body fiber / CAMKK-AMPK signaling cascade / ATPase-coupled monoatomic cation transmembrane transporter activity / ankyrin binding / response to ATP / potassium ion import across plasma membrane ...response to resveratrol / ATP-activated inward rectifier potassium channel activity / inward rectifying potassium channel / ventricular cardiac muscle tissue development / cell body fiber / CAMKK-AMPK signaling cascade / ATPase-coupled monoatomic cation transmembrane transporter activity / ankyrin binding / response to ATP / potassium ion import across plasma membrane / response to testosterone / action potential / axolemma / intercalated disc / negative regulation of insulin secretion / cellular response to nutrient levels / heat shock protein binding / T-tubule / acrosomal vesicle / response to ischemia / determination of adult lifespan / positive regulation of protein localization to plasma membrane / cellular response to glucose stimulus / cellular response to nicotine / nuclear envelope / cellular response to tumor necrosis factor / response to estradiol / presynaptic membrane / transmembrane transporter binding / response to hypoxia / endosome / response to xenobiotic stimulus / neuronal cell body / apoptotic process / glutamatergic synapse / ATP binding
Similarity search - Function
Potassium channel, inwardly rectifying, Kir6.2 / 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 / Immunoglobulin E-set
Similarity search - Domain/homology
ATP-sensitive inward rectifier potassium channel 11
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZhao C / MacKinnon R
Funding support1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Molecular structure of an open human K channel.
Authors: Chen Zhao / Roderick MacKinnon /
Abstract: K channels are metabolic sensors that translate intracellular ATP/ADP balance into membrane excitability. The molecular composition of K includes an inward-rectifier potassium channel (Kir) and an ...K channels are metabolic sensors that translate intracellular ATP/ADP balance into membrane excitability. The molecular composition of K includes an inward-rectifier potassium channel (Kir) and an ABC transporter-like sulfonylurea receptor (SUR). Although structures of K have been determined in many conformations, in all cases, the pore in Kir is closed. Here, we describe human pancreatic K (hK) structures with an open pore at 3.1- to 4.0-Å resolution using single-particle cryo-electron microscopy (cryo-EM). Pore opening is associated with coordinated structural changes within the ATP-binding site and the channel gate in Kir. Conformational changes in SUR are also observed, resulting in an area reduction of contact surfaces between SUR and Kir. We also observe that pancreatic hK exhibits the unique (among inward-rectifier channels) property of PIP-independent opening, which appears to be correlated with a docked cytoplasmic domain in the absence of PIP.
History
DepositionSep 12, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7s5t
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7s5t
  • Imaged by Jmol
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Structure viewerEM map:
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Supplemental images

emd_24839.png

Downloads & links

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Map

FileDownload / File: emd_24839.map.gz / Format: CCP4 / Size: 184 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap focus-refined on Kir and SUR TMD0 after sharpening (B-factor: 77.1)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 364 pix.
= 473.2 Å		1.3 Å/pix.
x 364 pix.
= 473.2 Å		1.3 Å/pix.
x 364 pix.
= 473.2 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: 0.7 / Movie #1: 0.7
Minimum - Maximum-2.71168 - 5.1525636
Average (Standard dev.)-0.0045080706 (±0.06521427)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions364364364
Spacing364364364
CellA=B=C: 473.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z364364364
origin x/y/z0.0000.0000.000
length x/y/z473.200473.200473.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-140-140-140
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS364364364
D min/max/mean-2.7125.153-0.005

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Supplemental data

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Sample components

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Entire : Human KATP channel composed of Kir6.2 (C166S G334D) and SUR1

EntireName: Human KATP channel composed of Kir6.2 (C166S G334D) and SUR1
Components
  • Complex: Human KATP channel composed of Kir6.2 (C166S G334D) and SUR1
    • Protein or peptide: ATP-sensitive inward rectifier potassium channel 11
  • Ligand: POTASSIUM ION

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Supramolecule #1: Human KATP channel composed of Kir6.2 (C166S G334D) and SUR1

SupramoleculeName: Human KATP channel composed of Kir6.2 (C166S G334D) and SUR1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 881.87 kDa/nm

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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: Homo sapiens (human)
Molecular weightTheoretical: 43.622746 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLSRKGIIPE EYVLTRLAED PAKPRYRARQ RRARFVSKKG NCNVAHKNIR EQGRFLQDVF TTLVDLKWPH TLLIFTMSFL CSWLLFAMA WWLIAFAHGD LAPSEGTAEP CVTSIHSFSS AFLFSIEVQV TIGFGGRMVT EECPLAILIL IVQNIVGLMI N AIMLGSIF ...String:
MLSRKGIIPE EYVLTRLAED PAKPRYRARQ RRARFVSKKG NCNVAHKNIR EQGRFLQDVF TTLVDLKWPH TLLIFTMSFL CSWLLFAMA WWLIAFAHGD LAPSEGTAEP CVTSIHSFSS AFLFSIEVQV TIGFGGRMVT EECPLAILIL IVQNIVGLMI N AIMLGSIF MKTAQAHRRA ETLIFSKHAV IALRHGRLCF MLRVGDLRKS MIISATIHMQ VVRKTTSPEG EVVPLHQVDI PM ENGVGGN SIFLVAPLII YHVIDANSPL YDLAPSDLHH HQDLEIIVIL EGVVETTGIT TQARTSYLAD EILWGQRFVP IVA EEDGRY SVDYSKFDNT VKVPTPLCTA RQLDEDHSLL EALTLASARG PLRKRSVPMA KAKPKFSISP DSLS

UniProtKB: ATP-sensitive inward rectifier potassium channel 11

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Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: K
Molecular weightTheoretical: 39.098 Da

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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

Concentration6.83 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 57.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Details: symmetry expanded in C4 / Number images used: 151967
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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