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- EMDB-55592: Structure of heteromeric mouse LRRC8A/D Volume-Regulated Anion Ch... -

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Basic information

Entry
Database: EMDB / ID: EMD-55592
TitleStructure of heteromeric mouse LRRC8A/D Volume-Regulated Anion Channel in complex with synthetic nanobody Sb4
Map data
Sample
  • Complex: Heteromeric LRRC8A/D in complex with Sb4
    • Protein or peptide: Volume-regulated anion channel subunit LRRC8A
    • Protein or peptide: Volume-regulated anion channel subunit LRRC8D
    • Protein or peptide: Volume-regulated anion channel subunit LRRC8D
  • Ligand: 1,2-ETHANEDIOL
KeywordsHeteromeric LRRC8A-D in complex with Sb4 / cell swelling / MEMBRANE PROTEIN
Function / homology
Function and homology information


Miscellaneous transport and binding events / pre-B cell differentiation / volume-sensitive anion channel activity / aspartate transmembrane transport / cyclic-GMP-AMP transmembrane transporter activity / cyclic-GMP-AMP transmembrane import across plasma membrane / monoatomic anion transmembrane transport / taurine transmembrane transport / cell volume homeostasis / monoatomic anion transport ...Miscellaneous transport and binding events / pre-B cell differentiation / volume-sensitive anion channel activity / aspartate transmembrane transport / cyclic-GMP-AMP transmembrane transporter activity / cyclic-GMP-AMP transmembrane import across plasma membrane / monoatomic anion transmembrane transport / taurine transmembrane transport / cell volume homeostasis / monoatomic anion transport / cellular response to osmotic stress / protein hexamerization / response to osmotic stress / monoatomic ion channel complex / positive regulation of myoblast differentiation / intracellular glucose homeostasis / chloride transmembrane transport / positive regulation of insulin secretion / spermatogenesis / lysosomal membrane / endoplasmic reticulum membrane / cell surface / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
LRRC8, pannexin-like TM region / Pannexin-like TM region of LRRC8 / : / : / Leucine-rich repeat region / 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. ...LRRC8, pannexin-like TM region / Pannexin-like TM region of LRRC8 / : / : / Leucine-rich repeat region / 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 / Volume-regulated anion channel subunit LRRC8A
Similarity search - Component
Biological speciesMus musculus (house mouse) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.97 Å
AuthorsLehmann EF / Deneka D / Stierli F / Rutz S / Dutzler R
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: Structures of the volume-regulated anion channel LRRC8A/D in activating and inhibiting conditions
Authors: Lehmann EF / Deneka D / Stierli F / Rutz S / Dutzler R
History
DepositionNov 5, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55592.png

Downloads & links

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Map

FileDownload / File: emd_55592.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.44 Å/pix.
x 336 pix.
= 483.84 Å		1.44 Å/pix.
x 336 pix.
= 483.84 Å		1.44 Å/pix.
x 336 pix.
= 483.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.44 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.232
Minimum - Maximum-0.3589787 - 1.0440084
Average (Standard dev.)-0.00040287746 (±0.021856664)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 483.84003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_55592_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55592_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Heteromeric LRRC8A/D in complex with Sb4

EntireName: Heteromeric LRRC8A/D in complex with Sb4
Components
  • Complex: Heteromeric LRRC8A/D in complex with Sb4
    • Protein or peptide: Volume-regulated anion channel subunit LRRC8A
    • Protein or peptide: Volume-regulated anion channel subunit LRRC8D
    • Protein or peptide: Volume-regulated anion channel subunit LRRC8D
  • Ligand: 1,2-ETHANEDIOL

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Supramolecule #1: Heteromeric LRRC8A/D in complex with Sb4

SupramoleculeName: Heteromeric LRRC8A/D in complex with Sb4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Volume-regulated anion channel subunit LRRC8A

MacromoleculeName: Volume-regulated anion channel subunit LRRC8A / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 93.753867 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSIPVTELRY FADTQPAYRI LKPWWDVFTD YISIVMLMIA VFGGTLQVTQ DKMICLPCKW VTKDSCNDSF RGWAASSPEP TYPNSTVLP TPDTGPTGIK YDLDRHQYNY VDAVCYENRL HWFAKYFPYL VLLHTLIFLA CSNFWFKFPR TSSKLEHFVS I LLKCFDSP ...String:
MSIPVTELRY FADTQPAYRI LKPWWDVFTD YISIVMLMIA VFGGTLQVTQ DKMICLPCKW VTKDSCNDSF RGWAASSPEP TYPNSTVLP TPDTGPTGIK YDLDRHQYNY VDAVCYENRL HWFAKYFPYL VLLHTLIFLA CSNFWFKFPR TSSKLEHFVS I LLKCFDSP WTTRALSETV VEESDPKPAF SKMNGSMDKK SSTVSEDVEA TVPMLQRTKS RIEQGIVDRS ETGVLDKKEG EQ AKALFEK VKKFRTHVEE GDIVYRLYMR QTIIKVIKFA LIICYTVYYV HNIKFDVDCT VDIESLTGYR TYRCAHPLAT LFK ILASFY ISLVIFYGLI CMYTLWWMLR RSLKKYSFES IREESSYSDI PDVKNDFAFM LHLIDQYDPL YSKRFAVFLS EVSE NKLRQ LNLNNEWTLD KLRQRLTKNA QDKLELHLFM LSGIPDTVFD LVELEVLKLE LIPDVTIPPS IAQLTGLKEL WLYHT AAKI EAPALAFLRE NLRALHIKFT DIKEIPLWIY SLKTLEELHL TGNLSAENNR YIVIDGLREL KRLKVLRLKS NLSKLP QVV TDVGVHLQKL SINNEGTKLI VLNSLKKMVN LTELELIRCD LERIPHSIFS LHNLQEIDLK DNNLKTIEEI ISFQHLH RL TCLKLWYNHI AYIPIQIGNL TNLERLYLNR NKIEKIPTQL FYCRKLRYLD LSHNNLTFLP ADIGLLQNLQ NLAVTANR I EALPPELFQC RKLRALHLGN NVLQSLPSRV GELTNLTQIE LRGNRLECLP VELGECPLLK RSGLVVEEDL FSTLPPEVK ERLWRA

UniProtKB: Volume-regulated anion channel subunit LRRC8A

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Macromolecule #2: Volume-regulated anion channel subunit LRRC8D

MacromoleculeName: Volume-regulated anion channel subunit LRRC8D / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 52.503219 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 EWT

UniProtKB: Volume-regulated anion channel subunit LRRC8D

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Macromolecule #3: Volume-regulated anion channel subunit LRRC8D

MacromoleculeName: Volume-regulated anion channel subunit LRRC8D / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.891195 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GPSQVQLVES GGGSVQAGGS LRLSCAASGY IYQIEYLGWF RQAPGKEREG VAALATWNGQ TYYADSVKGR FTVSLDNAKN TVYLQMNSL KPEDTALYYC AAAYEGDTSP LYYEEYGYWG QGTQVTVSA

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Macromolecule #4: 1,2-ETHANEDIOL

MacromoleculeName: 1,2-ETHANEDIOL / type: ligand / ID: 4 / Number of copies: 2 / Formula: EDO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 62.068 Da
Chemical component information

ChemComp-EDO:
1,2-ETHANEDIOL

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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

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 61.39 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 111259
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9t5p:
Structure of heteromeric mouse LRRC8A/D Volume-Regulated Anion Channel in complex with synthetic nanobody Sb4

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