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- EMDB-55589: Structure of mouse full-length LRRC8D -

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Basic information

Entry
Database: EMDB / ID: EMD-55589
TitleStructure of mouse full-length LRRC8D
Map data
Sample
  • Complex: Mouse full-length LRRC8D
    • Protein or peptide: Volume-regulated anion channel subunit LRRC8D
KeywordsTransmembrane protein / cell swelling / MEMBRANE PROTEIN
Function / homology
Function and homology information


Miscellaneous transport and binding events / volume-sensitive anion channel activity / aspartate transmembrane transport / monoatomic anion transmembrane transport / taurine transmembrane transport / monoatomic ion channel complex / cellular response to osmotic stress / protein hexamerization / intracellular glucose homeostasis / endoplasmic reticulum membrane ...Miscellaneous transport and binding events / volume-sensitive anion channel activity / aspartate transmembrane transport / monoatomic anion transmembrane transport / taurine transmembrane transport / monoatomic ion channel complex / cellular response to osmotic stress / protein hexamerization / intracellular glucose homeostasis / endoplasmic reticulum membrane / membrane / 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 LRRC8D
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsLehmann EF / Deneka D / Stierli F / Rutz S / Dutzler R
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Nat Commun / Year: 2026
Title: Structures of the volume-regulated anion channel LRRC8A/D in activating and inhibiting conditions.
Authors: Elena F Lehmann / Fabienne Stierli / Sonja Rutz / Dawid Deneka / Raimund Dutzler /
Abstract: Volume-regulated anion channels, which are activated in response to hypotonicity, are heteromers composed of LRRC8 family members. They consist of the obligatory subunit LRRC8A and at least another ...Volume-regulated anion channels, which are activated in response to hypotonicity, are heteromers composed of LRRC8 family members. They consist of the obligatory subunit LRRC8A and at least another paralog that determines their substrate preference. Here we investigate heteromeric assemblies composed of LRRC8A and D subunits, the latter of which confer permeability to amino acids, osmolytes and anti-cancer drugs. Using patch-clamp electrophysiology, we show that LRRC8A/D channels are reversibly activated by cell swelling and that their response is modulated by sybodies targeting the A subunits, which either potentiate or repress channel activity. Structures of the LRRC8A/D channel in complex with the inhibitory sybody Sb1 define the channel stoichiometry of four A and two D subunits, with Sb1 stabilizing the A subunits in a similar closed channel conformation as found in homomeric LRRC8A assemblies. In LRRC8A/D heteromers, the two D subunits weaken the arrangement of A subunits and thus enhance the activation properties of the channel. This channel conformation is strongly perturbed upon binding of the potentiating sybody Sb4, which disrupts the packing of the cytoplasmic domains linking their mobility to pore opening.
History
DepositionNov 5, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55589.png

Downloads & links

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Map

FileDownload / File: emd_55589.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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Contrast
Others
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

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.302 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.111
Minimum - Maximum-0.6011972 - 1.5369933
Average (Standard dev.)-0.00077012763 (±0.027500859)
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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Half map: #1

Fileemd_55589_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55589_half_map_2.map
Projections & Slices
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Sample components

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Entire : Mouse full-length LRRC8D

EntireName: Mouse full-length LRRC8D
Components
  • Complex: Mouse full-length LRRC8D
    • Protein or peptide: Volume-regulated anion channel subunit LRRC8D

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Supramolecule #1: Mouse full-length LRRC8D

SupramoleculeName: Mouse full-length LRRC8D / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 105.298 KDa

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Macromolecule #1: Volume-regulated anion channel subunit LRRC8D

MacromoleculeName: Volume-regulated anion channel subunit LRRC8D / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 105.429789 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSFTLAEVAS LNDIQPTYRI LKPWWDVFMD YLAVVMLMVA IFAGTMQLTK DQVVCLPVLP SPANSKAHTP PGNADVTTEV PRMETATHQ DQNGQTTTND VAFGTSAVTP DIPLQATHPH AESTLPNQEV KKEKRDPTGR KTNLDFQQYV FINQMCYHLA L PWYSKYFP ...String:
MSFTLAEVAS LNDIQPTYRI LKPWWDVFMD YLAVVMLMVA IFAGTMQLTK DQVVCLPVLP SPANSKAHTP PGNADVTTEV PRMETATHQ DQNGQTTTND VAFGTSAVTP DIPLQATHPH AESTLPNQEV KKEKRDPTGR KTNLDFQQYV FINQMCYHLA L PWYSKYFP YLALIHTIIL MVSSNFWFKY PKTCSKVEHF VSILGKCFES PWTTKALSET ACEDSEENKQ RITGAQTLPK HV STSSDEG SPSASTPMIN KTGFKFSAEK PVIEVPSMTI LDKKDGEQAK ALFEKVRKFR AHVEDSDLIY KLYVVQTVIK TAK FIFILC YTANFVNAIS FEHVCKPKVE HLIGYEVFEC THNMAYMLKK LLISYISIIC VYGFICLYTL FWLFRIPLKE YSFE KVREE SSFSDIPDVK NDFAFLLHMV DQYDQLYSKR FGVFLSEVSE NKLREISLNH EWTFEKLRQH VSRNAQDKQE LHLFM LSGV PDAVFDLTDL DVLKLELIPE AKIPAKISQM TNLQELHLCH CPAKVEQTAF SFLRDHLRCL HVKFTDVAEI PAWVYL LKN LRELYLIGNL NSENNKMIGL ESLRELRHLK ILHVKSNLTK VPSNITDVAP HLTKLVIHND GTKLLVLNSL KKMMNVA EL ELQNCELERI PHAIFSLSNL QELDLKSNNI RTIEEIISFQ HLKRLTCLKL WHNKIVAIPP SITHVKNLES LYFSNNKL E SLPTAVFSLQ KLRCLDVSYN NISTIPIEIG LLQNLQHLHI TGNKVDILPK QLFKCVKLRT LNLGQNCIAS LPEKISQLT QLTQLELKGN CLDRLPAQLG QCRMLKKSGL VVEDQLFDTL PLEVKEALNQ DVNVPFANGI ALEVLFQGPQ GTEQKLISEE DLRGASMDE KTTGWRGGHV VEGLAGELEQ LRARLEHHPQ GQREP

UniProtKB: Volume-regulated anion channel subunit LRRC8D

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

Concentration4.5 mg/mL
BufferpH: 8.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 4 % / Chamber temperature: 273.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.285 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7p5v

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 530537
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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