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- PDB-6fnw: Structure of a volume-regulated anion channel of the LRRC8 family -

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Basic information

Entry
Database: PDB / ID: 6fnw
TitleStructure of a volume-regulated anion channel of the LRRC8 family
ComponentsVolume-regulated anion channel subunit LRRC8A
KeywordsMEMBRANE PROTEIN / ion channel / leucine-rich repeat domain
Function / homology
Function and homology information


Miscellaneous transport and binding events / pre-B cell differentiation / volume-sensitive anion channel activity / taurine transmembrane transport / monoatomic anion transmembrane transport / aspartate transmembrane transport / cyclic-GMP-AMP transmembrane transporter activity / cyclic-GMP-AMP transmembrane import across plasma membrane / monoatomic anion transport / cell volume homeostasis ...Miscellaneous transport and binding events / pre-B cell differentiation / volume-sensitive anion channel activity / taurine transmembrane transport / monoatomic anion transmembrane transport / aspartate transmembrane transport / cyclic-GMP-AMP transmembrane transporter activity / cyclic-GMP-AMP transmembrane import across plasma membrane / monoatomic anion transport / cell volume homeostasis / protein hexamerization / response to osmotic stress / monoatomic ion channel complex / intracellular glucose homeostasis / positive regulation of myoblast differentiation / chloride transmembrane transport / positive regulation of insulin secretion / spermatogenesis / lysosomal membrane / cell surface / signal transduction / membrane / identical protein binding / plasma membrane
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 LRRC8A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsDeneka, D. / Sawicka, M. / Lam, A.K.M. / Paulino, C. / Dutzler, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Switzerland
CitationJournal: Nature / Year: 2018
Title: Structure of a volume-regulated anion channel of the LRRC8 family.
Authors: Dawid Deneka / Marta Sawicka / Andy K M Lam / Cristina Paulino / Raimund Dutzler /
Abstract: Volume-regulated anion channels are activated in response to hypotonic stress. These channels are composed of closely related paralogues of the leucine-rich repeat-containing protein 8 (LRRC8) family ...Volume-regulated anion channels are activated in response to hypotonic stress. These channels are composed of closely related paralogues of the leucine-rich repeat-containing protein 8 (LRRC8) family that co-assemble to form hexameric complexes. Here, using cryo-electron microscopy and X-ray crystallography, we determine the structure of a homomeric channel of the obligatory subunit LRRC8A. This protein conducts ions and has properties in common with endogenous heteromeric channels. Its modular structure consists of a transmembrane pore domain followed by a cytoplasmic leucine-rich repeat domain. The transmembrane domain, which is structurally related to connexin proteins, is wide towards the cytoplasm but constricted on the outside by a structural unit that acts as a selectivity filter. An excess of basic residues in the filter and throughout the pore attracts anions by electrostatic interaction. Our work reveals the previously unknown architecture of volume-regulated anion channels and their mechanism of selective anion conduction.
History
DepositionFeb 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2May 30, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Volume-regulated anion channel subunit LRRC8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4035
Polymers48,1551
Non-polymers2484
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint14 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.130, 140.130, 42.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 48155.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal domain of mouse LRRC8A / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lrrc8a, Lrrc8 / Plasmid: pcDNA3.1 / Cell line (production host): HEK293S GNTI- / Production host: Homo sapiens (human) / References: UniProt: Q80WG5
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

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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: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 22% PEG 3350, 0.2M Na/K tartrate, 0.1M Bis-Tris propane pH 8.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1, 2.05
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
22.051
ReflectionResolution: 1.8→40.452 Å / Num. obs: 44375 / % possible obs: 100 % / Redundancy: 20.2 % / Net I/σ(I): 27.05
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 19.8 % / Mean I/σ(I) obs: 2.27 / Num. unique obs: 6557 / CC1/2: 0.9 / Rrim(I) all: 1.58 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→40.452 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.35
RfactorNum. reflection% reflection
Rfree0.2082 1995 4.63 %
Rwork0.1792 --
obs0.1805 43134 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→40.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3359 0 16 337 3712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133497
X-RAY DIFFRACTIONf_angle_d1.274744
X-RAY DIFFRACTIONf_dihedral_angle_d17.9572184
X-RAY DIFFRACTIONf_chiral_restr0.07564
X-RAY DIFFRACTIONf_plane_restr0.009602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84510.33681190.31592430X-RAY DIFFRACTION81
1.8451-1.89490.29571250.29072600X-RAY DIFFRACTION87
1.8949-1.95070.30011380.24822791X-RAY DIFFRACTION93
1.9507-2.01370.28841430.2372995X-RAY DIFFRACTION100
2.0137-2.08560.24311430.20422969X-RAY DIFFRACTION100
2.0856-2.16910.21721500.19933002X-RAY DIFFRACTION100
2.1691-2.26780.23441490.18983013X-RAY DIFFRACTION100
2.2678-2.38740.22251420.18923000X-RAY DIFFRACTION100
2.3874-2.5370.24521450.18563023X-RAY DIFFRACTION100
2.537-2.73280.24871450.18283008X-RAY DIFFRACTION100
2.7328-3.00770.2021460.17723065X-RAY DIFFRACTION100
3.0077-3.44280.20711490.16843015X-RAY DIFFRACTION100
3.4428-4.33670.17291470.14393076X-RAY DIFFRACTION100
4.3367-40.46220.18581540.17833152X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 16.738 Å / Origin y: -45.7676 Å / Origin z: -1.9617 Å
111213212223313233
T0.218 Å20.0278 Å20.0119 Å2-0.2225 Å2-0.0183 Å2--0.2934 Å2
L2.9994 °21.6065 °2-0.3231 °2-1.6946 °2-0.2071 °2--0.611 °2
S0.0469 Å °0.0432 Å °0.4178 Å °0.0323 Å °0.0027 Å °0.1912 Å °-0.1378 Å °0.0207 Å °-0.0316 Å °
Refinement TLS groupSelection details: all

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