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- EMDB-15838: Cryo-EM structure of heteromeric LRRC8A/C (1:3 co-transfected) Vo... -

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Basic information

Entry
Database: EMDB / ID: EMD-15838
TitleCryo-EM structure of heteromeric LRRC8A/C (1:3 co-transfected) Volume-Regulated Anion Channel in complex with synthetic nanobody Sb1
Map data
Sample
  • Complex: Heteromeric LRRC8A/C Volume-Regulated Anion Channel in complex with synthetic nanobody Sb1
    • Complex: Heteromeric LRRC8A/C Volume-Regulated Anion Channel
    • Complex: Synthetic nanobody Sb1
Biological speciesMus musculus (house mouse) / Synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.5 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_15838.png

Downloads & links

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Map

FileDownload / File: emd_15838.map.gz / Format: CCP4 / Size: 18.1 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.)
2.6 Å/pix.
x 168 pix.
= 437.472 Å		2.6 Å/pix.
x 168 pix.
= 437.472 Å		2.6 Å/pix.
x 168 pix.
= 437.472 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.604 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.053541232 - 0.14612398
Average (Standard dev.)0.00083473686 (±0.0064147054)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 437.47202 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_15838_half_map_1.map
Projections & Slices
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Density Histograms

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Half map: #2

Fileemd_15838_half_map_2.map
Projections & Slices
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Sample components

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Entire : Heteromeric LRRC8A/C Volume-Regulated Anion Channel in complex wi...

EntireName: Heteromeric LRRC8A/C Volume-Regulated Anion Channel in complex with synthetic nanobody Sb1
Components
  • Complex: Heteromeric LRRC8A/C Volume-Regulated Anion Channel in complex with synthetic nanobody Sb1
    • Complex: Heteromeric LRRC8A/C Volume-Regulated Anion Channel
    • Complex: Synthetic nanobody Sb1

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Supramolecule #1: Heteromeric LRRC8A/C Volume-Regulated Anion Channel in complex wi...

SupramoleculeName: Heteromeric LRRC8A/C Volume-Regulated Anion Channel in complex with synthetic nanobody Sb1
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#5

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Supramolecule #2: Heteromeric LRRC8A/C Volume-Regulated Anion Channel

SupramoleculeName: Heteromeric LRRC8A/C Volume-Regulated Anion Channel / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: Synthetic nanobody Sb1

SupramoleculeName: Synthetic nanobody Sb1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Synthetic construct (others)

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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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 67.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 98883
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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