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- PDB-9ezc: Structure of the extracellular subdomain of a homomeric LRRC8C tr... -

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Basic information

Entry
Database: PDB / ID: 9ezc
TitleStructure of the extracellular subdomain of a homomeric LRRC8C truncation disease mutant
ComponentsVolume-regulated anion channel subunit LRRC8C
KeywordsMEMBRANE PROTEIN / Anion channel / Volume regulation / disease mutation
Function / homology
Function and homology information


Miscellaneous transport and binding events / volume-sensitive anion channel activity / aspartate transmembrane transport / taurine transmembrane transport / cyclic-GMP-AMP transmembrane import across plasma membrane / monoatomic anion transmembrane transport / protein hexamerization / cellular response to osmotic stress / fat cell differentiation / monoatomic ion channel complex ...Miscellaneous transport and binding events / volume-sensitive anion channel activity / aspartate transmembrane transport / taurine transmembrane transport / cyclic-GMP-AMP transmembrane import across plasma membrane / monoatomic anion transmembrane transport / protein hexamerization / cellular response to osmotic stress / fat cell differentiation / monoatomic ion channel complex / intracellular signal transduction / endoplasmic reticulum membrane / membrane / plasma membrane / cytoplasm
Similarity search - Function
LRRC8, pannexin-like TM region / Pannexin-like TM region of LRRC8 / : / 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 speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsRutz, S. / Quinodoz, M. / Peter, V. / Garavelli, L. / Innes, M.A. / Kellenberger, S. / Peng, Z. / Barone, A. / Campos-Xavier, B. / Unger, S. ...Rutz, S. / Quinodoz, M. / Peter, V. / Garavelli, L. / Innes, M.A. / Kellenberger, S. / Peng, Z. / Barone, A. / Campos-Xavier, B. / Unger, S. / Rivolta, C. / Dutzler, R. / Superti-Furga, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationNo. 310030_204373 Switzerland
CitationJournal: To Be Published
Title: Genetic activation of Volume-Regulated Anion Channels cause a multisystem disorder
Authors: Rutz, S. / Quinodoz, M. / Peter, V. / Garavelli, L. / Innes, M.A. / Kellenberger, S. / Peng, Z. / Barone, A. / Campos-Xavier, B. / Unger, S. / Rivolta, C. / Dutzler, R. / Superti-Furga, A.
History
DepositionApr 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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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
E: Volume-regulated anion channel subunit LRRC8C
F: Volume-regulated anion channel subunit LRRC8C
G: Volume-regulated anion channel subunit LRRC8C


Theoretical massNumber of molelcules
Total (without water)334,0407
Polymers334,0407
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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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: 47719.941 Da / Num. of mol.: 7 / Mutation: Leu400IlefsTer8
Source method: isolated from a genetically manipulated source
Details: The compound only shows the extracellular subdomain (ESD) of the channel
Source: (gene. exp.) Homo sapiens (human) / Gene: LRRC8C, AD158, FAD158 / Production host: Homo sapiens (human) / References: UniProt: Q8TDW0
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Homomeric LRRC8C truncation disease mutant / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 65 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 224687 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 50.47 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00325894
ELECTRON MICROSCOPYf_angle_d0.87347945
ELECTRON MICROSCOPYf_chiral_restr0.0519875
ELECTRON MICROSCOPYf_plane_restr0.0042973
ELECTRON MICROSCOPYf_dihedral_angle_d4.9954749

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