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- PDB-9t5r: LRR domain structure of the LRRC8D protein -

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Basic information

Entry
Database: PDB / ID: 9t5r
TitleLRR domain structure of the LRRC8D protein
ComponentsVolume-regulated anion channel subunit LRRC8D
KeywordsCYTOSOLIC PROTEIN / Cytosolic domain of LRRC8D
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 / cellular response to osmotic stress / protein hexamerization / monoatomic ion channel complex / 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 / cellular response to osmotic stress / protein hexamerization / monoatomic ion channel complex / 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
S,S-(2-HYDROXYETHYL)THIOCYSTEINE / Volume-regulated anion channel subunit LRRC8D
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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 LRRC8D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2022
Polymers47,0051
Non-polymers1971
Water5,873326
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19010 Å2
Unit cell
Length a, b, c (Å)36.855, 89.535, 143.698
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Volume-regulated anion channel subunit LRRC8D / Leucine-rich repeat-containing protein 5 / Leucine-rich repeat-containing protein 8D


Mass: 47004.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lrrc8d, Lrrc5 / Production host: Homo sapiens (human) / References: UniProt: Q8BGR2
#2: Chemical ChemComp-CME / S,S-(2-HYDROXYETHYL)THIOCYSTEINE


Type: L-peptide linking / Mass: 197.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO3S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M malonate and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→44.8 Å / Num. obs: 63729 / % possible obs: 96.35 % / Redundancy: 26.1 % / Biso Wilson estimate: 38.38 Å2 / Rmerge(I) obs: 9.8 / Net I/σ(I): 22.43
Reflection shellResolution: 1.96→1.99 Å / Rmerge(I) obs: 9.8 / Num. unique obs: 34115

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419+SVNrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→44.77 Å / SU ML: 0.3005 / Cross valid method: FREE R-VALUE / σ(F): 1.17 / Phase error: 26.1183
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2263 3200 5.02 %
Rwork0.1936 60529 -
obs0.1952 63729 96.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.32 Å2
Refinement stepCycle: LAST / Resolution: 1.96→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3267 0 0 326 3593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073374
X-RAY DIFFRACTIONf_angle_d0.8464567
X-RAY DIFFRACTIONf_chiral_restr0.0524548
X-RAY DIFFRACTIONf_plane_restr0.0054578
X-RAY DIFFRACTIONf_dihedral_angle_d17.39361298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.990.49821410.43152681X-RAY DIFFRACTION98.43
1.99-2.020.31581470.32652772X-RAY DIFFRACTION100
2.02-2.050.29961410.29432736X-RAY DIFFRACTION99.97
2.05-2.090.28511410.27932699X-RAY DIFFRACTION99.68
2.09-2.120.28871420.23252719X-RAY DIFFRACTION100
2.12-2.170.26911440.23272783X-RAY DIFFRACTION100
2.17-2.210.26211420.24712677X-RAY DIFFRACTION100
2.21-2.260.6032660.51681210X-RAY DIFFRACTION44.76
2.26-2.310.34941200.29712213X-RAY DIFFRACTION80.42
2.31-2.370.2331430.21872676X-RAY DIFFRACTION100
2.37-2.430.23851490.19942751X-RAY DIFFRACTION100
2.43-2.50.2221400.19572720X-RAY DIFFRACTION100
2.5-2.580.22711460.19272713X-RAY DIFFRACTION99.93
2.58-2.680.25771470.20222758X-RAY DIFFRACTION99.79
2.68-2.780.24461460.19192695X-RAY DIFFRACTION99.41
2.78-2.910.24841380.20892713X-RAY DIFFRACTION100
2.91-3.060.25781490.2152780X-RAY DIFFRACTION100
3.06-3.260.2251420.20062687X-RAY DIFFRACTION100
3.26-3.510.23141420.19082726X-RAY DIFFRACTION99.97
3.51-3.860.25681430.1832675X-RAY DIFFRACTION97.24
3.86-4.420.15121440.14332690X-RAY DIFFRACTION99.09
4.42-5.570.16921460.14472722X-RAY DIFFRACTION99.38
5.57-44.770.18231410.16152733X-RAY DIFFRACTION99.79
Refinement TLS params.Method: refined / Origin x: 12.9775567688 Å / Origin y: -19.8341581707 Å / Origin z: -33.4026580496 Å
111213212223313233
T0.253834248571 Å2-0.0217273297547 Å2-0.0606337347928 Å2-0.269124433307 Å2-0.00599660494532 Å2--0.315362004743 Å2
L0.380708074901 °20.185715210401 °2-0.308302203277 °2-0.966822982951 °2-0.511226911286 °2--1.2573375505 °2
S-0.079829210908 Å °-0.0371828488916 Å °0.00106692457801 Å °-0.218335420781 Å °0.0199352864893 Å °0.0224574726352 Å °0.0751561679247 Å °0.0978288850896 Å °0.0537568109267 Å °
Refinement TLS groupSelection details: all

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