[English] 日本語
Yorodumi
- PDB-6baa: Cryo-EM structure of the pancreatic beta-cell KATP channel bound ... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6baa
TitleCryo-EM structure of the pancreatic beta-cell KATP channel bound to ATP and glibenclamide
DescriptorATP-sensitive inward rectifier potassium channel 11
ATP-binding cassette sub-family C member 8
KeywordsMETAL TRANSPORT / KATP / SUR1 / Kir6.2 / sulfonylurea receptor
Specimen sourceRattus norvegicus / mammal / Rat / ドブネズミ, どぶねずみ /
Cricetus cricetus / mammal / Black-bellied hamster / クロハラハムスクー, ヨーロッパハムスター
MethodElectron microscopy (3.63 Å resolution / Particle / Single particle)
AuthorsMartin, G.M. / Yoshioka, C. / Shyng, S.L.
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 Report
SummaryFull reportAbout validation report
DateDeposition: Oct 12, 2017 / Release: Nov 1, 2017

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
A: ATP-sensitive inward rectifier potassium channel 11
B: ATP-sensitive inward rectifier potassium channel 11
C: ATP-sensitive inward rectifier potassium channel 11
D: ATP-sensitive inward rectifier potassium channel 11
E: ATP-binding cassette sub-family C member 8
F: ATP-binding cassette sub-family C member 8
G: ATP-binding cassette sub-family C member 8
H: ATP-binding cassette sub-family C member 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)887,92216
Polyers883,9178
Non-polymers4,0058
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)41760
ΔGint (kcal/M)-312
Surface area (Å2)299500

-
Components

#1: Polypeptide(L)
ATP-sensitive inward rectifier potassium channel 11 / BIR / Inward rectifier K(+) channel Kir6.2 / Potassium channel / inwardly rectifying subfamily J member 11


Mass: 43645.719 Da / Num. of mol.: 4
Source: (gene. exp.) Rattus norvegicus / mammal / ドブネズミ, どぶねずみ /
References: UniProt: P70673
#2: Polypeptide(L)
ATP-binding cassette sub-family C member 8 / Sulfonylurea receptor 1


Mass: 177333.578 Da / Num. of mol.: 4
Source: (gene. exp.) Cricetus cricetus / mammal / クロハラハムスクー, ヨーロッパハムスター
References: UniProt: Q09427
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / ATP (energy-carrying molecule) *YM


Mass: 507.181 Da / Num. of mol.: 4 / Formula: C10H16N5O13P3
#4: Chemical
ChemComp-GBM / 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide / Glibenclamide, Glyburide


Mass: 494.004 Da / Num. of mol.: 4 / Formula: C23H28ClN3O5S

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

-
Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1Pancreatic beta-cell ATP-sensitive K+ channel (KATP)COMPLEX1, 20RECOMBINANT
2ATP-sensitive K+ channel subunit Kir6.2COMPLEX11RECOMBINANT
3ATP-binding cassette sub-family C member 8COMPLEX21RECOMBINANT
Molecular weightValue: 0.95 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
1110116Rattus norvegicus
2110034Cricetus cricetus
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
1110116Rattus norvegicus
2110116Rattus norvegicus
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4
3D reconstructionResolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 59417 / Symmetry type: POINT

+
About Yorodumi

-
News

-
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

-
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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more