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- EMDB-15835: Cryo-EM structure of homomeric LRRC8C Volume-Regulated Anion Channel -

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Basic information

Entry
Database: EMDB / ID: EMD-15835
TitleCryo-EM structure of homomeric LRRC8C Volume-Regulated Anion Channel
Map data
Sample
  • Complex: Homomeric LRRC8C Volume-Regulated Anion Channel
    • Protein or peptide: Volume-regulated anion channel subunit LRRC8C
Function / homology
Function and homology information


Miscellaneous transport and binding events / volume-sensitive anion channel activity / taurine transmembrane transport / monoatomic anion transmembrane transport / aspartate transmembrane transport / cyclic-GMP-AMP transmembrane import across plasma membrane / cellular response to osmotic stress / protein hexamerization / monoatomic ion channel complex / fat cell differentiation ...Miscellaneous transport and binding events / volume-sensitive anion channel activity / taurine transmembrane transport / monoatomic anion transmembrane transport / aspartate transmembrane transport / cyclic-GMP-AMP transmembrane import across plasma membrane / cellular response to osmotic stress / protein hexamerization / monoatomic ion channel complex / fat cell differentiation / endoplasmic reticulum membrane / endoplasmic reticulum / signal transduction / plasma membrane / cytoplasm
Similarity search - Function
LRRC8, pannexin-like TM region / Pannexin-like TM region of LRRC8 / Leucine Rich Repeat / 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 LRRC8C
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsSawicka M / Dutzler R
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Structure of a volume-regulated heteromeric LRRC8A/C channel.
Authors: Sonja Rutz / Dawid Deneka / Antje Dittmann / Marta Sawicka / Raimund Dutzler /
Abstract: Volume-regulated anion channels (VRACs) participate in the cellular response to osmotic swelling. These membrane proteins consist of heteromeric assemblies of LRRC8 subunits, whose compositions ...Volume-regulated anion channels (VRACs) participate in the cellular response to osmotic swelling. These membrane proteins consist of heteromeric assemblies of LRRC8 subunits, whose compositions determine permeation properties. Although structures of the obligatory LRRC8A, also referred to as SWELL1, have previously defined the architecture of VRACs, the organization of heteromeric channels has remained elusive. Here we have addressed this question by the structural characterization of murine LRRC8A/C channels. Like LRRC8A, these proteins assemble as hexamers. Despite 12 possible arrangements, we find a predominant organization with an A:C ratio of two. In this assembly, four LRRC8A subunits cluster in their preferred conformation observed in homomers, as pairs of closely interacting proteins that stabilize a closed state of the channel. In contrast, the two interacting LRRC8C subunits show a larger flexibility, underlining their role in the destabilization of the tightly packed A subunits, thereby enhancing the activation properties of the protein.
History
DepositionSep 19, 2022-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateFeb 1, 2023-
Current statusFeb 1, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15835.png

Downloads & links

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Map

FileDownload / File: emd_15835.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 336 pix.
= 437.472 Å		1.3 Å/pix.
x 336 pix.
= 437.472 Å		1.3 Å/pix.
x 336 pix.
= 437.472 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.302 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.007181508 - 0.03186789
Average (Standard dev.)9.8719e-05 (±0.0008038702)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 437.47202 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Masked transmembrane region at 4.1 A

Fileemd_15835_additional_1.map
AnnotationMasked transmembrane region at 4.1 A
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_15835_half_map_1.map
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Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_15835_half_map_2.map
Projections & Slices
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Sample components

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Entire : Homomeric LRRC8C Volume-Regulated Anion Channel

EntireName: Homomeric LRRC8C Volume-Regulated Anion Channel
Components
  • Complex: Homomeric LRRC8C Volume-Regulated Anion Channel
    • Protein or peptide: Volume-regulated anion channel subunit LRRC8C

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Supramolecule #1: Homomeric LRRC8C Volume-Regulated Anion Channel

SupramoleculeName: Homomeric LRRC8C Volume-Regulated Anion Channel / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Volume-regulated anion channel subunit LRRC8C

MacromoleculeName: Volume-regulated anion channel subunit LRRC8C / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 93.472594 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSIPVTEFRQ FSEQQPAFRV LKPWWDVFTD YLSVAMLMIG VFGCTLQVMQ DKIICLPKRV QPAQNHSSVP NVSQAVISTT PLPPPKPSP TNPATVEMKG LKTDLDLQQY SFINQMCYER ALHWYAKYFP YLVLIHTLVF MLCSNFWFKF PGSSSKIEHF I SILGKCFD ...String:
MSIPVTEFRQ FSEQQPAFRV LKPWWDVFTD YLSVAMLMIG VFGCTLQVMQ DKIICLPKRV QPAQNHSSVP NVSQAVISTT PLPPPKPSP TNPATVEMKG LKTDLDLQQY SFINQMCYER ALHWYAKYFP YLVLIHTLVF MLCSNFWFKF PGSSSKIEHF I SILGKCFD SPWTTRALSE VSGEDSEEKD NRKNNMNRSG TIQSGPEGNL VRSQSLKSIP EKFVVDKSAA GALDKKEGEQ AK ALFEKVK KFRLHVEEGD ILYAMYVRQT VLKVIKFLII IAYNSALVSK VQFTVDCNVD IQDMTGYKNF SCNHTMAHLF SKL SFCYLC FVSIYGLTCL YTLYWLFYRS LREYSFEYVR QETGIDDIPD VKNDFAFMLH MIDQYDPLYS KRFAVFLSEV SENK LKQLN LNNEWTPDKL RQKLQTNAHN RLELPLIMLS GLPDTVFEIT ELQSLKLEII KNVMIPATIA QLDNLQELCL HQCSV KIHS AALSFLKENL KVLSVKFDDM RELPPWMYGL RNLEELYLVG SLSHDISKNV TLESLRDLKS LKILSIKSNV SKIPQA VVD VSSHLQKMCV HNDGTKLVML NNLKKMTNLT ELELVHCDLE RIPHAVFSLL SLQELDLKEN NLKSIEEIVS FQHLRKL TV LKLWYNSIAY IPEHIKKLTS LERLFFSHNK VEVLPSHLFL CNKIRYLDLS YNDIRFIPPE IGVLQSLQYF SITCNKVE S LPDELYFCKK LKTLKIGKNS LSVLSPKIGN LLFLSYLDIK GNHFEVLPPE LGDCRALKRA RLVVEDALFE TLPSDVREQ MKADALEVLF Q

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8.5
VitrificationCryogen name: ETHANE-PROPANE

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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: 2.4 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 137432
FSC plot (resolution estimation)

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