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Yorodumi- PDB-7p5y: Structure of homomeric LRRC8A Volume-Regulated Anion Channel in c... -
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-Basic information
Entry | Database: PDB / ID: 7p5y | ||||||
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Title | Structure of homomeric LRRC8A Volume-Regulated Anion Channel in complex with synthetic nanobody Sb3 | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / LRRC8 family / Volume-Regulated Anion Channel / leucine-rich repeat / sybody / cryo-EM | ||||||
Function / homology | Function and homology information Miscellaneous transport and binding events / pre-B cell differentiation / volume-sensitive anion channel activity / taurine transmembrane transport / aspartate transmembrane transport / cyclic-GMP-AMP transmembrane transporter activity / cyclic-GMP-AMP transmembrane import across plasma membrane / monoatomic anion transmembrane transport / cell volume homeostasis / protein hexamerization ...Miscellaneous transport and binding events / pre-B cell differentiation / volume-sensitive anion channel activity / taurine transmembrane transport / aspartate transmembrane transport / cyclic-GMP-AMP transmembrane transporter activity / cyclic-GMP-AMP transmembrane import across plasma membrane / monoatomic anion transmembrane transport / cell volume homeostasis / protein hexamerization / monoatomic anion transport / 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 / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.29 Å | ||||||
Authors | Deneka, D. / Rutz, S. / Sawicka, M. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Allosteric modulation of LRRC8 channels by targeting their cytoplasmic domains. Authors: Dawid Deneka / Sonja Rutz / Cedric A J Hutter / Markus A Seeger / Marta Sawicka / Raimund Dutzler / Abstract: Members of the LRRC8 family form heteromeric assemblies, which function as volume-regulated anion channels. These modular proteins consist of a transmembrane pore and cytoplasmic leucine-rich repeat ...Members of the LRRC8 family form heteromeric assemblies, which function as volume-regulated anion channels. These modular proteins consist of a transmembrane pore and cytoplasmic leucine-rich repeat (LRR) domains. Despite their known molecular architecture, the mechanism of activation and the role of the LRR domains in this process has remained elusive. Here we address this question by generating synthetic nanobodies, termed sybodies, which target the LRR domain of the obligatory subunit LRRC8A. We use these binders to investigate their interaction with homomeric LRRC8A channels by cryo-electron microscopy and the consequent effect on channel activation by electrophysiology. The five identified sybodies either inhibit or enhance activity by binding to distinct epitopes of the LRR domain, thereby altering channel conformations. In combination, our work provides a set of specific modulators of LRRC8 proteins and reveals the role of their cytoplasmic domains as regulators of channel activity by allosteric mechanisms. | ||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 7p5y.cif.gz | 860.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p5y.ent.gz | 740.9 KB | Display | PDB format |
PDBx/mmJSON format | 7p5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p5y_validation.pdf.gz | 821.2 KB | Display | wwPDB validaton report |
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Full document | 7p5y_full_validation.pdf.gz | 894.9 KB | Display | |
Data in XML | 7p5y_validation.xml.gz | 125.2 KB | Display | |
Data in CIF | 7p5y_validation.cif.gz | 178.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/7p5y ftp://data.pdbj.org/pub/pdb/validation_reports/p5/7p5y | HTTPS FTP |
-Related structure data
Related structure data | 13208MC 7p5vC 7p5wC 7p60C 7p6kC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 94239.383 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lrrc8a, Lrrc8 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q80WG5 #2: Antibody | Mass: 16450.988 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli MC1061 (bacteria) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Homomeric LRRC8A Volume-Regulated Anion Channel in complex with synthetic nanobody Sb3 Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 67 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.1_4122: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73350 / Symmetry type: POINT | ||||||||||||||||||||||||
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