[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
Components
  • ATP-binding cassette sub-family C member 8
  • ATP-sensitive inward rectifier potassium channel 11
KeywordsMETAL TRANSPORT / KATP / SUR1 / Kir6.2 / sulfonylurea receptor
Function / homologyInward rectifier potassium channel C-terminal domain / P-loop containing nucleoside triphosphate hydrolase / ATP-binding cassette subfamily C member 8 / Potassium channel, inwardly rectifying, Kir6.2 / ABC transporter-like / AAA+ ATPase domain / ABC transporter type 1, transmembrane domain / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Immunoglobulin E-set / Potassium channel, inwardly rectifying, Kir ...Inward rectifier potassium channel C-terminal domain / P-loop containing nucleoside triphosphate hydrolase / ATP-binding cassette subfamily C member 8 / Potassium channel, inwardly rectifying, Kir6.2 / ABC transporter-like / AAA+ ATPase domain / ABC transporter type 1, transmembrane domain / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Immunoglobulin E-set / Potassium channel, inwardly rectifying, Kir / ABC transporter, conserved site / Sulphonylurea receptor / ABC transporter type 1, transmembrane domain superfamily / ABC transporter transmembrane region / Ion homeostasis / ABC-family proteins mediated transport / ATP sensitive Potassium channels / ABC transporter integral membrane type-1 fused domain profile. / ATP-binding cassette, ABC transporter-type domain profile. / Inward rectifier potassium channel transmembrane domain / ABC transporters family signature. / ABC transporter / ATP-activated inward rectifier potassium channel activity / sulfonylurea receptor activity / inward rectifying potassium channel / cell body fiber / nervous system process / go:0010107: / positive regulation of cation channel activity / cellular response to nicotine / ankyrin binding / response to ATP / axolemma / potassium channel activity / ATPase activity, coupled to transmembrane movement of substances / intercalated disc / response to testosterone / regulation of membrane potential / response to ischemia / T-tubule / negative regulation of insulin secretion / acrosomal vesicle / heat shock protein binding / cellular response to glucose stimulus / potassium ion transport / positive regulation of protein localization to plasma membrane / sarcolemma / nuclear envelope / glucose metabolic process / cellular response to tumor necrosis factor / response to estradiol / ion channel binding / protein C-terminus binding / endosome / response to drug / intracellular membrane-bounded organelle / myelin sheath / neuronal cell body / endoplasmic reticulum / mitochondrion / integral component of membrane / ATP binding / plasma membrane / cytosol / ATP-sensitive inward rectifier potassium channel 11 / ATP-binding cassette sub-family C member 8
Function and homology information
Specimen sourceRattus norvegicus (Norway rat)
Cricetus cricetus (black-bellied hamster)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.63 Å resolution
AuthorsMartin, G.M. / Yoshioka, C. / Shyng, S.L.
CitationJournal: Elife / Year: 2017
Title: Anti-diabetic drug binding site in a mammalian K channel revealed by Cryo-EM.
Authors: 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
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 1, 2017Structure modelrepositoryInitial release
1.1Feb 28, 2018Structure modelDatabase referencescitation_citation.title
1.2Mar 28, 2018Structure modelData collection / Database referencescitation_citation.title

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-7073
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

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: Protein/peptide
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 (Norway rat) / Gene: Kcnj11 / Cell line (production host): INS-1 / Production host: Rattus norvegicus (Norway rat) / References: UniProt: P70673
#2: Protein/peptide
ATP-binding cassette sub-family C member 8 / Sulfonylurea receptor 1


Mass: 177333.578 Da / Num. of mol.: 4
Source: (gene. exp.) Cricetus cricetus (black-bellied hamster)
Gene: ABCC8, SUR / Production host: Rattus norvegicus (Norway rat) / References: UniProt: Q09427
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#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 / Glibenclamide

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

-
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 MDa / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
1110116Rattus norvegicus (Norway rat)
2110034Cricetus cricetus (black-bellied hamster)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
1110116Rattus norvegicus (Norway rat)
2110116Rattus norvegicus (Norway rat)
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 FIELDBright-field microscopy
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

-
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

+
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

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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