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- EMDB-7073: Cryo-EM structure of the pancreatic beta-cell KATP channel bound ... -

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Basic information

Entry
Database: EMDB / ID: 7073
TitleCryo-EM structure of the pancreatic beta-cell KATP channel bound to ATP and glibenclamide
SamplePancreatic beta-cell ATP-sensitive K+ channel (KATP)
SourceRattus norvegicus / mammal / ドブネズミ, どぶねずみ /
Map datalow-pass filtered and sharpened with B-factor of -50, pancreatic beta-cell KATP channel bound to ATP and glibenclamide
Methodsingle particle reconstruction, at 3.63 Å resolution
AuthorsMartin GM / Yoshioka C
CitationElife, 2017, 6

Elife, 2017, 6 Yorodumi Papers
Anti-diabetic drug binding site in a mammalian KATP channel revealed by Cryo-EM.
Gregory M Martin / Balamurugan Kandasamy / Frank DiMaio / Craig Yoshioka / Show-Ling Shyng

Validation ReportPDB-ID: 6baa

SummaryFull reportAbout validation report
DateDeposition: Oct 12, 2017 / Header (metadata) release: Nov 1, 2017 / Map release: Nov 1, 2017 / Last update: Nov 1, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 5
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6baa
  • Surface level: 5
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_7073.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
0.86 Å/pix.
= 256.5 Å
300 pix
0.86 Å/pix.
= 256.5 Å
300 pix
0.86 Å/pix.
= 256.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 0.855 Å
Density
Contour Level:5 (by author), 5 (movie #1):
Minimum - Maximum-9.947775 - 21.047916
Average (Standard dev.)0.16722862 (1.3686122)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin000
Limit299299299
Spacing300300300
CellA=B=C: 256.5 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8550.8550.855
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z256.500256.500256.500
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-9.94821.0480.167

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Supplemental data

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Mask #1

Fileemd_7073_msk_1.map ( map file in CCP4 format, 108001 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Annotation detailsmask used for final cisTEM refinement. Can be used to regenerate sharpened maps from unfiltered map, pancreatic beta-cell KATP channel bound to ATP and glibenclamide
Space group number1

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Mask #1~

Fileemd_7073_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Pancreatic beta-cell ATP-sensitive K+ channel (KATP)

EntireName: Pancreatic beta-cell ATP-sensitive K+ channel (KATP) / Number of components: 7
MassTheoretical: 950 kDa

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Component #1: protein, Pancreatic beta-cell ATP-sensitive K+ channel (KATP)

ProteinName: Pancreatic beta-cell ATP-sensitive K+ channel (KATP) / Recombinant expression: No
MassTheoretical: 950 kDa
SourceSpecies: Rattus norvegicus / mammal / ドブネズミ, どぶねずみ /
Source (engineered)Expression System: Rattus norvegicus / mammal / ドブネズミ, どぶねずみ /

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Component #2: protein, ATP-sensitive K+ channel subunit Kir6.2

ProteinName: ATP-sensitive K+ channel subunit Kir6.2 / Recombinant expression: No

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Component #3: protein, ATP-binding cassette sub-family C member 8

ProteinName: ATP-binding cassette sub-family C member 8 / Recombinant expression: No

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

ProteinName: ATP-sensitive inward rectifier potassium channel 11 / Recombinant expression: No
MassTheoretical: 43.645719 kDa
Source (engineered)Expression System: Rattus norvegicus / mammal / ドブネズミ, どぶねずみ /

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

ProteinName: ATP-binding cassette sub-family C member 8 / Recombinant expression: No
MassTheoretical: 177.333578 kDa
Source (engineered)Expression System: Cricetus cricetus / mammal / クロハラハムスクー, ヨーロッパハムスター

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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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Component #7: ligand, 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}e...

LigandName: 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.494004 kDa

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Experimental details

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Sample preparation

Specimen stateparticle
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: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 59417
3D reconstructionResolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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