[English] 日本語
Yorodumi
- EMDB-27773: Structure of LRRC8C-LRRC8A(IL125) Chimera, Class 4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-27773
TitleStructure of LRRC8C-LRRC8A(IL125) Chimera, Class 4
Map data
Sample
  • Complex: LRRC8C-LRRC8A(IL125) chimera
    • Protein or peptide: Volume-regulated anion channel subunit LRRC8C,Volume-regulated anion channel subunit LRRC8A
Function / homology
Function and homology information


Miscellaneous transport and binding events / pre-B cell differentiation / volume-sensitive anion channel activity / taurine transmembrane transport / aspartate transmembrane transport / monoatomic anion transmembrane transport / cyclic-GMP-AMP transmembrane transporter activity / cyclic-GMP-AMP transmembrane import across plasma membrane / cellular response to osmotic stress / monoatomic anion transport ...Miscellaneous transport and binding events / pre-B cell differentiation / volume-sensitive anion channel activity / taurine transmembrane transport / aspartate transmembrane transport / monoatomic anion transmembrane transport / cyclic-GMP-AMP transmembrane transporter activity / cyclic-GMP-AMP transmembrane import across plasma membrane / cellular response to osmotic stress / monoatomic anion transport / cell volume homeostasis / protein hexamerization / response to osmotic stress / monoatomic ion channel complex / fat cell differentiation / intracellular glucose homeostasis / positive regulation of myoblast differentiation / chloride transmembrane transport / positive regulation of insulin secretion / spermatogenesis / lysosomal membrane / endoplasmic reticulum membrane / cell surface / signal transduction / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
LRRC8, pannexin-like TM region / Pannexin-like TM region of LRRC8 / Leucine-rich repeat, SDS22-like subfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Volume-regulated anion channel subunit LRRC8A / Volume-regulated anion channel subunit LRRC8C
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsTakahashi H / Yamada T / Denton JS / Strange K / Karakas E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK51610 United States
CitationJournal: Elife / Year: 2023
Title: Cryo-EM structures of an LRRC8 chimera with native functional properties reveal heptameric assembly.
Authors: Hirohide Takahashi / Toshiki Yamada / Jerod S Denton / Kevin Strange / Erkan Karakas /
Abstract: Volume-regulated anion channels (VRACs) mediate volume regulatory Cl and organic solute efflux from vertebrate cells. VRACs are heteromeric assemblies of LRRC8A-E proteins with unknown ...Volume-regulated anion channels (VRACs) mediate volume regulatory Cl and organic solute efflux from vertebrate cells. VRACs are heteromeric assemblies of LRRC8A-E proteins with unknown stoichiometries. Homomeric LRRC8A and LRRC8D channels have a small pore, hexameric structure. However, these channels are either non-functional or exhibit abnormal regulation and pharmacology, limiting their utility for structure-function analyses. We circumvented these limitations by developing novel homomeric LRRC8 chimeric channels with functional properties consistent with those of native VRAC/LRRC8 channels. We demonstrate here that the LRRC8C-LRRC8A(IL1) chimera comprising LRRC8C and 25 amino acids unique to the first intracellular loop (IL1) of LRRC8A has a heptameric structure like that of homologous pannexin channels. Unlike homomeric LRRC8A and LRRC8D channels, heptameric LRRC8C-LRRC8A(IL1) channels have a large-diameter pore similar to that estimated for native VRACs, exhibit normal DCPIB pharmacology, and have higher permeability to large organic anions. Lipid-like densities are located between LRRC8C-LRRC8A(IL1) subunits and occlude the channel pore. Our findings provide new insights into VRAC/LRRC8 channel structure and suggest that lipids may play important roles in channel gating and regulation.
History
DepositionAug 2, 2022-
Header (metadata) releaseMar 22, 2023-
Map releaseMar 22, 2023-
UpdateMar 22, 2023-
Current statusMar 22, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_27773.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.83804876 - 1.230313
Average (Standard dev.)-0.0008262046 (±0.022546424)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 396.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Unsharpened map.

Fileemd_27773_additional_1.map
AnnotationUnsharpened map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: #2

Fileemd_27773_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: #1

Fileemd_27773_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

-
Entire : LRRC8C-LRRC8A(IL125) chimera

EntireName: LRRC8C-LRRC8A(IL125) chimera
Components
  • Complex: LRRC8C-LRRC8A(IL125) chimera
    • Protein or peptide: Volume-regulated anion channel subunit LRRC8C,Volume-regulated anion channel subunit LRRC8A

-
Supramolecule #1: LRRC8C-LRRC8A(IL125) chimera

SupramoleculeName: LRRC8C-LRRC8A(IL125) chimera / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all / Details: Heptameric LRRC8C-LRRC8A(IL125) chimera.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 700 KDa

-
Macromolecule #1: Volume-regulated anion channel subunit LRRC8C,Volume-regulated an...

MacromoleculeName: Volume-regulated anion channel subunit LRRC8C,Volume-regulated anion channel subunit LRRC8A
type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 94.747695 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MIPVTEFRQF SEQQPAFRVL KPWWDVFTDY LSVAMLMIGV FGCTLQVMQD KIICLPKRVQ PAQNHSSLSN VSQAVASTTP LPPPKPSPA NPITVEMKGL KTDLDLQQYS FINQMCYERA LHWYAKYFPY LVLIHTLVFM LCSNFWFKFP GSSSKIEHFI S ILGKCFDS ...String:
MIPVTEFRQF SEQQPAFRVL KPWWDVFTDY LSVAMLMIGV FGCTLQVMQD KIICLPKRVQ PAQNHSSLSN VSQAVASTTP LPPPKPSPA NPITVEMKGL KTDLDLQQYS FINQMCYERA LHWYAKYFPY LVLIHTLVFM LCSNFWFKFP GSSSKIEHFI S ILGKCFDS PWTTRALSEV SGEDSDPKPA FSKMNGSMDK KSSTVSEDVE GSLVNSQSLK SIPEKFVVDK STAGALDKKE GE QAKALFE KVKKFRLHVE EGDILYAMYV RQTVLKVIKF LIIIAYNSAL VSKVQFTVDC NVDIQDMTGY KNFSCNHTMA HLF SKLSFC YLCFVSIYGL TCLYTLYWLF YRSLREYSFE YVRQETGIDD IPDVKNDFAF MLHMIDQYDP LYSKRFAVFL SEVS ENKLK QLNLNNEWTP DKLRQKLQTN AHNRLELPLI MLSGLPDTVF EITELQSLKL EIIKNVMIPA TIAQLDNLQE LSLHQ CSVK IHSAALSFLK ENLKVLSVKF DDMRELPPWM YGLRNLEELY LVGSLSHDIS RNVTLESLRD LKSLKILSIK SNVSKI PQA VVDVSSHLQK MCIHNDGTKL VMLNNLKKMT NLTELELVHC DLERIPHAVF SLLSLQELDL KENNLKSIEE IVSFQHL RK LTVLKLWHNS ITYIPEHIKK LTSLERLSFS HNKIEVLPSH LFLCNKIRYL DLSYNDIRFI PPEIGVLQSL QYFSITCN V ESLPDELYFC KKLKTLKIGK NSLSVLSPKI GNLLFLSYLD VKGNHFEILP PELGDCRALK RAGLVVEDAL FETLPSDVR EQMKTEENLY FQGAAAGDYK DDDDK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.0 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
0.15 MNaClSodium chlorideSodium chloride
0.05 MTris-HClTrisTris buffer pH 8.0
0.005 %LMNGLMNG detergent
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 3198 / Average electron dose: 54.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 846122
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationNumber classes: 6
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 93179
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8dxq:
Structure of LRRC8C-LRRC8A(IL125) Chimera, Class 4

+
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