[English] 日本語
Yorodumi
- PDB-8qql: Cryo-EM structure of the human inward-rectifier potassium 2.1 cha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qql
TitleCryo-EM structure of the human inward-rectifier potassium 2.1 channel (Kir2.1) - R312H mutant
ComponentsInward rectifier potassium channel 2
KeywordsMEMBRANE PROTEIN / Ion channel / Potassium Channel / Kir channel
Function / homology
Function and homology information


Sensory perception of sour taste / Classical Kir channels / regulation of skeletal muscle contraction via regulation of action potential / relaxation of skeletal muscle / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / magnesium ion transport / membrane repolarization during action potential / Phase 4 - resting membrane potential / membrane repolarization during cardiac muscle cell action potential / regulation of membrane repolarization ...Sensory perception of sour taste / Classical Kir channels / regulation of skeletal muscle contraction via regulation of action potential / relaxation of skeletal muscle / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / magnesium ion transport / membrane repolarization during action potential / Phase 4 - resting membrane potential / membrane repolarization during cardiac muscle cell action potential / regulation of membrane repolarization / membrane depolarization during cardiac muscle cell action potential / regulation of resting membrane potential / positive regulation of potassium ion transmembrane transport / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / cardiac muscle cell action potential involved in contraction / intracellular potassium ion homeostasis / regulation of cardiac muscle cell contraction / relaxation of cardiac muscle / potassium ion import across plasma membrane / regulation of heart rate by cardiac conduction / intercalated disc / voltage-gated potassium channel complex / phosphatidylinositol-4,5-bisphosphate binding / potassium ion transmembrane transport / T-tubule / potassium ion transport / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / cellular response to mechanical stimulus / protein homotetramerization / dendritic spine / postsynaptic membrane / neuronal cell body / glutamatergic synapse / identical protein binding / membrane / plasma membrane
Similarity search - Function
Potassium channel, inwardly rectifying, Kir2.1 / Potassium channel, inwardly rectifying, Kir, N-terminal / Inward rectifier potassium channel N-terminal / 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
Inward rectifier potassium channel 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6 Å
AuthorsFernandes, C.A.H. / Zuniga, D. / Venien-Bryan, C.
Funding support France, European Union, 2items
OrganizationGrant numberCountry
The French Muscular Dystrophy Telethon (AFM-Telethon)#23207 France
H2020 Marie Curie Actions of the European Commission101026386European Union
CitationJournal: FASEB J / Year: 2024
Title: Biochemical, biophysical, and structural investigations of two mutants (C154Y and R312H) of the human Kir2.1 channel involved in the Andersen-Tawil syndrome.
Authors: Dania Zuniga / Andreas Zoumpoulakis / Rafael F Veloso / Laurie Peverini / Sophie Shi / Alexandre Pozza / Valérie Kugler / Françoise Bonneté / Tahar Bouceba / Renaud Wagner / Pierre-Jean ...Authors: Dania Zuniga / Andreas Zoumpoulakis / Rafael F Veloso / Laurie Peverini / Sophie Shi / Alexandre Pozza / Valérie Kugler / Françoise Bonneté / Tahar Bouceba / Renaud Wagner / Pierre-Jean Corringer / Carlos A H Fernandes / Catherine Vénien-Bryan /
Abstract: Inwardly rectifying potassium (Kir) channels play a pivotal role in physiology by establishing, maintaining, and regulating the resting membrane potential of the cells, particularly contributing to ...Inwardly rectifying potassium (Kir) channels play a pivotal role in physiology by establishing, maintaining, and regulating the resting membrane potential of the cells, particularly contributing to the cellular repolarization of many excitable cells. Dysfunction in Kir2.1 channels is implicated in several chronic and debilitating human diseases for which there are currently no effective treatments. Specifically, Kir2.1-R312H and Kir2.1-C154Y mutations are associated with Andersen-Tawil syndrome (ATS) in humans. We have investigated the impact of these two mutants in the trafficking of the channel to the cell membrane and function in Xenopus laevis oocytes. Despite both mutations being trafficked to the cell membrane at different extents and capable of binding PIP (phosphatidylinositol-4,5-bisphosphate), the main modulator for channel activity, they resulted in defective channels that do not display K current, albeit through different molecular mechanisms. Coexpression studies showed that R312H and C154Y are expressed and associated with the WT subunits. While WT subunits could rescue R312H dysfunction, the presence of a unique C154Y subunit disrupts the function of the entire complex, which is a typical feature of mutations with a dominant-negative effect. Molecular dynamics simulations showed that Kir2.1-C154Y mutation induces a loss in the structural plasticity of the selectivity filter, impairing the K flow. In addition, the cryo-EM structure of the Kir2.1-R312H mutant has been reconstructed. This study identified the molecular mechanisms by which two ATS-causing mutations impact Kir2.1 channel function and provide valuable insights that can guide potential strategies for the development of future therapeutic interventions for ATS.
History
DepositionOct 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Inward rectifier potassium channel 2
C: Inward rectifier potassium channel 2
D: Inward rectifier potassium channel 2
A: Inward rectifier potassium channel 2


Theoretical massNumber of molelcules
Total (without water)144,5954
Polymers144,5954
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein
Inward rectifier potassium channel 2 / Cardiac inward rectifier potassium channel / Inward rectifier K(+) channel Kir2.1 / IRK-1 / hIRK1 / ...Cardiac inward rectifier potassium channel / Inward rectifier K(+) channel Kir2.1 / IRK-1 / hIRK1 / Potassium channel / inwardly rectifying subfamily J member 2


Mass: 36148.816 Da / Num. of mol.: 4 / Mutation: R312H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNJ2, IRK1 / Production host: Komagataella pastoris (fungus) / References: UniProt: P63252
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Human inward-rectifier potassium 2.1 channel (Kir2.1) containing the Andersen-syndrome related mutation R312H
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Komagataella pastoris (fungus)
Buffer solutionpH: 7.4
Details: 20 mM Tris-HCl pH 7.4, 150 mM KCl, 1 mM EDTA, 0.59 mM DDM
Buffer componentConc.: 20 mM / Name: Tris(hydroxymethyl)aminomethane hydrochloride / Formula: tris-hcl
SpecimenConc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Blotting force 0, blotting time 3s

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Details: Preliminary grid screening was performed manually at a Glacios 2 microscope.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.35 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10762
EM imaging opticsEnergyfilter name: TFS Selectris X

-
Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.2.1particle selection
2EPU2.11image acquisition
7PHENIX1.20.1_4487model fitting
8NAMD1model fittingOn-line version of NAMDinator software
10PHENIX1.20.1_4487model refinement
11cryoSPARC4.2.1initial Euler assignment
12cryoSPARC4.2.1final Euler assignment
13cryoSPARC4.2.1classification
14cryoSPARC4.2.13D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 2787753
Details: A blob picking followed by 2D classification was performed to generate templates for automated template-picking. Initially, 2,787,753 particles were selected after template-picking, which ...Details: A blob picking followed by 2D classification was performed to generate templates for automated template-picking. Initially, 2,787,753 particles were selected after template-picking, which were submitted to three rounds do 2D classification to remove false picks, ice contamination and classes with unclear features.
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146539 / Num. of class averages: 4 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 7zdz

7zdz


Accession code: 7zdz / Chain residue range: 195-367 / Pdb chain residue range: 195-367 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310096
ELECTRON MICROSCOPYf_angle_d0.82213684
ELECTRON MICROSCOPYf_dihedral_angle_d6.4511316
ELECTRON MICROSCOPYf_chiral_restr0.0491556
ELECTRON MICROSCOPYf_plane_restr0.0061716

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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