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- PDB-8ben: LRR domain Structure of the LRRC8C protein -

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Basic information

Entry
Database: PDB / ID: 8ben
TitleLRR domain Structure of the LRRC8C protein
ComponentsVolume-regulated anion channel subunit LRRC8C
KeywordsMEMBRANE PROTEIN / Ion channel / Volume-regulated anion channel
Function / homology
Function and homology information


Miscellaneous transport and binding events / volume-sensitive anion channel activity / taurine transmembrane transport / monoatomic anion transmembrane transport / aspartate transmembrane transport / cyclic-GMP-AMP transmembrane import across plasma membrane / cellular response to osmotic stress / protein hexamerization / monoatomic ion channel complex / fat cell differentiation ...Miscellaneous transport and binding events / volume-sensitive anion channel activity / taurine transmembrane transport / monoatomic anion transmembrane transport / aspartate transmembrane transport / cyclic-GMP-AMP transmembrane import across plasma membrane / cellular response to osmotic stress / protein hexamerization / monoatomic ion channel complex / fat cell differentiation / endoplasmic reticulum membrane / endoplasmic reticulum / signal transduction / plasma membrane / cytoplasm
Similarity search - Function
LRRC8, pannexin-like TM region / Pannexin-like TM region of LRRC8 / Leucine Rich Repeat / 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 LRRC8C
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSawicka, M. / Dutzler, R.
Funding support Switzerland, 1items
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
DepositionOct 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Volume-regulated anion channel subunit LRRC8C
B: Volume-regulated anion channel subunit LRRC8C
C: Volume-regulated anion channel subunit LRRC8C
D: Volume-regulated anion channel subunit LRRC8C


Theoretical massNumber of molelcules
Total (without water)188,7564
Polymers188,7564
Non-polymers00
Water0
1
A: Volume-regulated anion channel subunit LRRC8C


Theoretical massNumber of molelcules
Total (without water)47,1891
Polymers47,1891
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Volume-regulated anion channel subunit LRRC8C


Theoretical massNumber of molelcules
Total (without water)47,1891
Polymers47,1891
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Volume-regulated anion channel subunit LRRC8C


Theoretical massNumber of molelcules
Total (without water)47,1891
Polymers47,1891
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Volume-regulated anion channel subunit LRRC8C


Theoretical massNumber of molelcules
Total (without water)47,1891
Polymers47,1891
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.376, 104.726, 111.829
Angle α, β, γ (deg.)90.000, 94.710, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 396 through 526 or resid 535 through 801))
d_2ens_1(chain "B" and (resid 396 through 526 or resid 535 through 801))
d_3ens_1(chain "C" and (resid 396 through 526 or resid 535 through 801))
d_4ens_1(chain "D" and (resid 396 through 526 or resid 535 through 801))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERSERA1 - 131
d_12ens_1LEULYSA136 - 402
d_21ens_1SERSERB4 - 134
d_22ens_1LEULYSB139 - 405
d_31ens_1SERSERC2 - 132
d_32ens_1LEULYSC141 - 407
d_41ens_1SERSERD3 - 133
d_42ens_1LEULYSD135 - 401

NCS oper:
IDCodeMatrixVector
1given(0.366621852922, -0.905080694808, -0.215446867803), (0.928667042237, 0.370008388592, 0.0259097864718), (0.056266700841, -0.209577499407, 0.976171772855)21.9902248237, -23.8092640032, -25.0318662769
2given(-0.999985653993, -0.00523189312739, -0.00114852207021), (0.00524951204, -0.99985957381, -0.015914624864), (-0.00106509717118, -0.0159204257331, 0.999872694703)45.9089489024, -10.1057599132, -0.284182736637
3given(-0.373841427644, 0.902847882435, 0.212387118627), (-0.926529044967, -0.373965314741, -0.041156678723), (0.0422671954313, -0.212168905716, 0.976318513415)23.9281534204, 14.211493032, -24.2782493871

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Components

#1: Protein
Volume-regulated anion channel subunit LRRC8C / / Factor for adipocyte differentiation 158 / Leucine-rich repeat-containing protein 8C


Mass: 47189.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lrrc8c, Ad158, Fad158 / Production host: Homo sapiens (human) / References: UniProt: Q8R502

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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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M magnesium chloride, 20% PEG3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / 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: 3.1→49.19 Å / Num. obs: 30438 / % possible obs: 98.3 % / Redundancy: 7.2 % / Biso Wilson estimate: 30.53 Å2 / Rmerge(I) obs: 0.35 / Net I/σ(I): 5.53
Reflection shellResolution: 3.1→3.2 Å / Num. unique obs: 2773 / CC1/2: 0.76

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FNW

6fnw


Resolution: 3.1→49.19 Å / SU ML: 0.4184 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.7431
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2896 2006 6.59 %
Rwork0.2406 28432 -
obs0.2438 30438 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.32 Å2
Refinement stepCycle: LAST / Resolution: 3.1→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13038 0 0 0 13038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006613267
X-RAY DIFFRACTIONf_angle_d0.84117926
X-RAY DIFFRACTIONf_chiral_restr0.05642136
X-RAY DIFFRACTIONf_plane_restr0.00592234
X-RAY DIFFRACTIONf_dihedral_angle_d4.70621699
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.64988432868
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.00426990668
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.87584203392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.180.39371470.30632043X-RAY DIFFRACTION99.46
3.18-3.260.38621350.29262038X-RAY DIFFRACTION99.54
3.26-3.360.34881580.28722003X-RAY DIFFRACTION99.45
3.36-3.470.32231500.28812058X-RAY DIFFRACTION99.46
3.47-3.590.30961260.2752002X-RAY DIFFRACTION99.25
3.59-3.740.33031570.24982021X-RAY DIFFRACTION99.27
3.74-3.910.2781390.2222036X-RAY DIFFRACTION99.63
3.91-4.110.26751490.22372038X-RAY DIFFRACTION99.41
4.11-4.370.25991340.21642057X-RAY DIFFRACTION99.68
4.37-4.710.27261430.20332024X-RAY DIFFRACTION99.54
4.71-5.180.24491390.20091995X-RAY DIFFRACTION96.52
5.18-5.930.29231330.23471933X-RAY DIFFRACTION93.78
5.93-7.460.25131400.25012090X-RAY DIFFRACTION100
7.46-49.190.22131560.21342094X-RAY DIFFRACTION99.73

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