[English] 日本語
Yorodumi
- PDB-7zdz: Cryo-EM structure of the human inward-rectifier potassium 2.1 cha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zdz
TitleCryo-EM structure of the human inward-rectifier potassium 2.1 channel (Kir2.1)
ComponentsInward rectifier potassium channel 2
KeywordsMEMBRANE PROTEIN / Potassium channel / Inward-rectifier channel / inward rectification
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 / magnesium ion transport / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / Phase 4 - resting membrane potential / membrane repolarization during action 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 / magnesium ion transport / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / Phase 4 - resting membrane potential / membrane repolarization during action 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 / regulation of monoatomic ion transmembrane transport / inward rectifier potassium channel activity / positive regulation of potassium ion transmembrane transport / cardiac muscle cell action potential involved in contraction / regulation of cardiac muscle cell contraction / relaxation of cardiac muscle / potassium ion import across plasma membrane / intracellular potassium ion homeostasis / regulation of heart rate by cardiac conduction / intercalated disc / phosphatidylinositol-4,5-bisphosphate binding / voltage-gated potassium channel complex / potassium ion transmembrane transport / T-tubule / cellular response to mechanical stimulus / potassium ion transport / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / 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
: / STRONTIUM ION / Inward rectifier potassium channel 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsFernandes, C.A.H. / Venien-Bryan, C. / Fagnen, C. / Zuniga, D.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-11-EQPX-0008 France
The French Muscular Dystrophy Telethon (AFM-Telethon)23207 France
The French Muscular Dystrophy Telethon (AFM-Telethon)23210 France
CitationJournal: Sci Adv / Year: 2022
Title: Cryo-electron microscopy unveils unique structural features of the human Kir2.1 channel.
Authors: Carlos A H Fernandes / Dania Zuniga / Charline Fagnen / Valérie Kugler / Rosa Scala / Gérard Péhau-Arnaudet / Renaud Wagner / David Perahia / Saïd Bendahhou / Catherine Vénien-Bryan /
Abstract: We present the first structure of the human Kir2.1 channel containing both transmembrane domain (TMD) and cytoplasmic domain (CTD). Kir2.1 channels are strongly inward-rectifying potassium channels ...We present the first structure of the human Kir2.1 channel containing both transmembrane domain (TMD) and cytoplasmic domain (CTD). Kir2.1 channels are strongly inward-rectifying potassium channels that play a key role in maintaining resting membrane potential. Their gating is modulated by phosphatidylinositol 4,5-bisphosphate (PIP). Genetically inherited defects in Kir2.1 channels are responsible for several rare human diseases, including Andersen's syndrome. The structural analysis (cryo-electron microscopy), surface plasmon resonance, and electrophysiological experiments revealed a well-connected network of interactions between the PIP-binding site and the G-loop through residues R312 and H221. In addition, molecular dynamics simulations and normal mode analysis showed the intrinsic tendency of the CTD to tether to the TMD and a movement of the secondary anionic binding site to the membrane even without PIP. Our results revealed structural features unique to human Kir2.1 and provided insights into the connection between G-loop and gating and the pathological mechanisms associated with this channel.
History
DepositionMar 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)193,5917
Polymers193,3774
Non-polymers2143
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area24770 Å2
ΔGint-213 kcal/mol
Surface area67950 Å2

-
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: 48344.141 Da / Num. of mol.: 4
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
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sr / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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 channel 2.1 (Kir2.1) / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 50 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Komagataella pastoris (fungus)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMPotassium chlorideKCl1
220 mMTrizma hydrochlorideTris-HCl1
30.03 %Dodecyl-B-D-maltosideDDM1
41 mMEthylenediamine tetraacetic acidEDTA1
52 mMDichlorodiphenyltrichloroethaneDDT1
SpecimenConc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4 sec. / Electron dose: 61.7 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9895
Image scansSampling size: 10 µm / Width: 5760 / Height: 4092

-
Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
1crYOLO1.6particle selection
2EPUimage acquisition
4CTFFIND4CTF correction
7PHENIX1.2model fitting
9PHENIX1.2model refinement
10Coot0.9.7model refinement
11RELION3.0.7initial Euler assignment
12RELION3.0.7final Euler assignment
13RELION3.0.7classification
14RELION3.0.73D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1031472
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63584 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 404.73 / Protocol: OTHER / Space: REAL / Target criteria: Correlation coefficient
Details: For structural fitting, it was used dock-in-map (available at PHENIX) that uses both SSM and convolution-based shape searches to find a part of a map that is similar to a model. An initial ...Details: For structural fitting, it was used dock-in-map (available at PHENIX) that uses both SSM and convolution-based shape searches to find a part of a map that is similar to a model. An initial in silico homology model of human Kir2.1 was generated using I-TASSER using the crystal structure of chicken Kir2.2 channel (PDB ID 3JYC) as a template. For building and refinement of the atomic model, the transmembrane domain (TMD, 55-184 region) of this in silico model was placed into the final sharpened cryo-EM map using the Dock in Map tool available in PHENIX. For the cytoplasmic domain (CTD; 188-367 region), the crystal structure of the CTD from mice Kir2.1 channel (PDB ID 1U4F) was placed into the final cryo-EM map using the same approach. Once the models were placed in the electron density, the loops that connect the two domains (185-187 region) and a N-terminal loop (41-54 region) absent in the in silico model were manually built using Coot.
Atomic model buildingPDB-ID: 1U4F

1u4f


Accession code: 1U4F / Pdb chain residue range: 188-367 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310595
ELECTRON MICROSCOPYf_angle_d0.82814342
ELECTRON MICROSCOPYf_dihedral_angle_d4.7661393
ELECTRON MICROSCOPYf_chiral_restr0.0471616
ELECTRON MICROSCOPYf_plane_restr0.0031807

+
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