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- PDB-9t5q: LRR domain Structure of LRRC8A in complex with synthetic nanobody Sb4 -

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Basic information

Entry
Database: PDB / ID: 9t5q
TitleLRR domain Structure of LRRC8A in complex with synthetic nanobody Sb4
Components
  • Sb4
  • Volume-regulated anion channel subunit LRRC8A
KeywordsCYTOSOLIC PROTEIN / Cytosolic domain of LRRC8A in complex with Sb4
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 / 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 / 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 LRRC8A
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLehmann, E.F. / Deneka, D. / Stierli, F. / Rutz, S. / Dutzler, R.
Funding support Switzerland, 1items
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, E.F. / Deneka, D. / Stierli, F. / Rutz, S. / Dutzler, R.
History
DepositionNov 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Volume-regulated anion channel subunit LRRC8A
I: Sb4
B: Volume-regulated anion channel subunit LRRC8A
C: Sb4


Theoretical massNumber of molelcules
Total (without water)123,9254
Polymers123,9254
Non-polymers00
Water15,097838
1
A: Volume-regulated anion channel subunit LRRC8A
I: Sb4


Theoretical massNumber of molelcules
Total (without water)61,9622
Polymers61,9622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Volume-regulated anion channel subunit LRRC8A
C: Sb4


Theoretical massNumber of molelcules
Total (without water)61,9622
Polymers61,9622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.948, 73.486, 81.924
Angle α, β, γ (deg.)111.037, 94.349, 110.313
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

#1: Protein Volume-regulated anion channel subunit LRRC8A / Leucine-rich repeat-containing protein 8A / Protein ebouriffe / ebo / Swelling protein 1


Mass: 48071.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lrrc8a, Lrrc8, Swell1 / Production host: Homo sapiens (human) / References: UniProt: Q80WG5
#2: Antibody Sb4


Mass: 13891.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli MC1061 (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 838 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 4000, 10 % (v/v) 2-PropOH and 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS4 X 2M / Detector: PIXEL / Date: Mar 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→40.08 Å / Num. obs: 142196 / % possible obs: 96.96 % / Redundancy: 26.1 % / Rmerge(I) obs: 9.99 / Net I/σ(I): 11.74
Reflection shellResolution: 1.6→1.62 Å / Rmerge(I) obs: 9.99 / Num. unique obs: 142196

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419+SVNrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→40.08 Å / SU ML: 0.1822 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.1128
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2289 7109 5 %
Rwork0.1984 135087 -
obs0.1999 142196 96.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.96 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8423 0 0 838 9261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00578580
X-RAY DIFFRACTIONf_angle_d0.830611639
X-RAY DIFFRACTIONf_chiral_restr0.05281358
X-RAY DIFFRACTIONf_plane_restr0.00691471
X-RAY DIFFRACTIONf_dihedral_angle_d15.16433229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.33622280.26974334X-RAY DIFFRACTION95.4
1.62-1.640.28562350.26324453X-RAY DIFFRACTION95.01
1.64-1.660.30182320.264411X-RAY DIFFRACTION95.24
1.66-1.680.29272330.25084423X-RAY DIFFRACTION95.45
1.68-1.70.2522320.23184425X-RAY DIFFRACTION95.25
1.7-1.720.25692340.23714444X-RAY DIFFRACTION95.92
1.72-1.750.27732380.23074508X-RAY DIFFRACTION95.47
1.75-1.770.26482300.23534386X-RAY DIFFRACTION96.11
1.77-1.80.25112370.2164503X-RAY DIFFRACTION95.8
1.8-1.830.2452350.21214463X-RAY DIFFRACTION96.41
1.83-1.860.25472360.21454478X-RAY DIFFRACTION95.99
1.86-1.90.25852340.21864439X-RAY DIFFRACTION96.69
1.9-1.930.24752380.20734536X-RAY DIFFRACTION96.21
1.93-1.970.22742350.19614457X-RAY DIFFRACTION96.8
1.97-2.020.23372360.19344484X-RAY DIFFRACTION96.86
2.02-2.060.22262380.19484518X-RAY DIFFRACTION96.71
2.06-2.110.22252360.19044481X-RAY DIFFRACTION97.16
2.11-2.170.24682390.19544556X-RAY DIFFRACTION97.22
2.17-2.240.22212390.19624530X-RAY DIFFRACTION97.27
2.24-2.310.22992370.20124512X-RAY DIFFRACTION97.58
2.31-2.390.23822390.19774537X-RAY DIFFRACTION97.65
2.39-2.490.21722380.19884522X-RAY DIFFRACTION97.78
2.49-2.60.23492420.19894590X-RAY DIFFRACTION97.91
2.6-2.740.24542390.19824543X-RAY DIFFRACTION98.09
2.74-2.910.23612410.20124584X-RAY DIFFRACTION98.35
2.91-3.130.23512410.20564576X-RAY DIFFRACTION98.53
3.13-3.450.2082400.19644572X-RAY DIFFRACTION98.65
3.45-3.940.21722430.18234605X-RAY DIFFRACTION99.02
3.94-4.970.22420.16434601X-RAY DIFFRACTION99.18
4.97-40.080.19642420.19374616X-RAY DIFFRACTION99.2
Refinement TLS params.Method: refined / Origin x: -24.3178393707 Å / Origin y: 21.6644898522 Å / Origin z: -2.200373115 Å
111213212223313233
T0.129807655879 Å20.00363434865105 Å20.00994011381007 Å2-0.162029623411 Å2-0.00124365231773 Å2--0.171601469216 Å2
L0.0114638692854 °20.0167756423913 °20.0409141348589 °2-0.0693837995499 °20.0742004040709 °2--0.228767216059 °2
S-0.00823067022972 Å °0.00501426029367 Å °-0.00318963130932 Å °0.00442656754997 Å °-0.00701958952706 Å °0.00674960577511 Å °0.0179840577023 Å °-0.00778581799448 Å °0.0130921205517 Å °
Refinement TLS groupSelection details: all

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