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Yorodumi- EMDB-13202: Cryo-EM structure of homomeric LRRC8A Volume-Regulated Anion Chan... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13202 | |||||||||
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Title | Cryo-EM structure of homomeric LRRC8A Volume-Regulated Anion Channel in complex with synthetic nanobody Sb1 | |||||||||
Map data | full-length complex at 3.1 A | |||||||||
Sample |
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Keywords | LRRC8 family / Volume-Regulated Anion Channel / leucine-rich repeat / sybody / cryo-EM / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information pre-B cell differentiation / Miscellaneous transport and binding events / volume-sensitive anion channel activity / taurine transmembrane transport / cyclic-GMP-AMP transmembrane transporter activity / aspartate transmembrane transport / cyclic-GMP-AMP transmembrane import across plasma membrane / monoatomic anion transmembrane transport / cell volume homeostasis / protein hexamerization ...pre-B cell differentiation / Miscellaneous transport and binding events / volume-sensitive anion channel activity / taurine transmembrane transport / cyclic-GMP-AMP transmembrane transporter activity / aspartate transmembrane transport / 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 | single particle reconstruction / cryo EM / Resolution: 3.06 Å | |||||||||
Authors | Deneka D / Rutz S | |||||||||
Funding support | 1 items
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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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13202.map.gz | 11.2 MB | EMDB map data format | |
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Header (meta data) | emd-13202-v30.xml emd-13202.xml | 21.1 KB 21.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13202_fsc.xml | 11.9 KB | Display | FSC data file |
Images | emd_13202.png | 65.4 KB | ||
Masks | emd_13202_msk_1.map | 144.7 MB | Mask map | |
Filedesc metadata | emd-13202.cif.gz | 5.8 KB | ||
Others | emd_13202_additional_1.map.gz emd_13202_additional_2.map.gz emd_13202_additional_3.map.gz emd_13202_half_map_1.map.gz emd_13202_half_map_2.map.gz | 8.9 MB 9.7 MB 8.1 MB 8.4 MB 8.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13202 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13202 | HTTPS FTP |
-Validation report
Summary document | emd_13202_validation.pdf.gz | 536.6 KB | Display | EMDB validaton report |
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Full document | emd_13202_full_validation.pdf.gz | 536.3 KB | Display | |
Data in XML | emd_13202_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | emd_13202_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13202 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13202 | HTTPS FTP |
-Related structure data
Related structure data | 7p5vMC 7p5wC 7p5yC 7p60C 7p6kC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13202.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | full-length complex at 3.1 A | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.302 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_13202_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: masked transmembrane region at 2.7 A
File | emd_13202_additional_1.map | ||||||||||||
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Annotation | masked transmembrane region at 2.7 A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: masked cytoplasmic region including all leucine-rich repeat domains...
File | emd_13202_additional_2.map | ||||||||||||
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Annotation | masked cytoplasmic region including all leucine-rich repeat domains and bound Sb1 sybodies at 3.3 A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: masked region of a single pair of tightly...
File | emd_13202_additional_3.map | ||||||||||||
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Annotation | masked region of a single pair of tightly interacting leucine-rich repeat domains and bound Sb1 sybodies at 2.8 A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_13202_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_13202_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Homomeric LRRC8A Volume-Regulated Anion Channel in complex with s...
Entire | Name: Homomeric LRRC8A Volume-Regulated Anion Channel in complex with synthetic nanobody Sb1 |
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Components |
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-Supramolecule #1: Homomeric LRRC8A Volume-Regulated Anion Channel in complex with s...
Supramolecule | Name: Homomeric LRRC8A Volume-Regulated Anion Channel in complex with synthetic nanobody Sb1 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Macromolecule #1: Volume-regulated anion channel subunit LRRC8A
Macromolecule | Name: Volume-regulated anion channel subunit LRRC8A / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 94.239383 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MIPVTELRYF ADTQPAYRIL KPWWDVFTDY ISIVMLMIAV FGGTLQVTQD KMICLPCKWV TKDSCNDSFR GWAASSPEPT YPNSTVLPT PDTGPTGIKY DLDRHQYNYV DAVCYENRLH WFAKYFPYLV LLHTLIFLAC SNFWFKFPRT SSKLEHFVSI L LKCFDSPW ...String: MIPVTELRYF ADTQPAYRIL KPWWDVFTDY ISIVMLMIAV FGGTLQVTQD KMICLPCKWV TKDSCNDSFR GWAASSPEPT YPNSTVLPT PDTGPTGIKY DLDRHQYNYV DAVCYENRLH WFAKYFPYLV LLHTLIFLAC SNFWFKFPRT SSKLEHFVSI L LKCFDSPW TTRALSETVV EESDPKPAFS KMNGSMDKKS STVSEDVEAT VPMLQRTKSR IEQGIVDRSE TGVLDKKEGE QA KALFEKV KKFRTHVEEG DIVYRLYMRQ TIIKVIKFAL IICYTVYYVH NIKFDVDCTV DIESLTGYRT YRCAHPLATL FKI LASFYI SLVIFYGLIC MYTLWWMLRR SLKKYSFESI REESSYSDIP DVKNDFAFML HLIDQYDPLY SKRFAVFLSE VSEN KLRQL NLNNEWTLDK LRQRLTKNAQ DKLELHLFML SGIPDTVFDL VELEVLKLEL IPDVTIPPSI AQLTGLKELW LYHTA AKIE APALAFLREN LRALHIKFTD IKEIPLWIYS LKTLEELHLT GNLSAENNRY IVIDGLRELK RLKVLRLKSN LSKLPQ VVT DVGVHLQKLS INNEGTKLIV LNSLKKMVNL TELELIRCDL ERIPHSIFSL HNLQEIDLKD NNLKTIEEII SFQHLHR LT CLKLWYNHIA YIPIQIGNLT NLERLYLNRN KIEKIPTQLF YCRKLRYLDL SHNNLTFLPA DIGLLQNLQN LAVTANRI E ALPPELFQCR KLRALHLGNN VLQSLPSRVG ELTNLTQIEL RGNRLECLPV ELGECPLLKR SGLVVEEDLF STLPPEVKE RLWRADKEQA UniProtKB: Volume-regulated anion channel subunit LRRC8A |
-Macromolecule #2: Synthetic nanobody Sb1
Macromolecule | Name: Synthetic nanobody Sb1 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 16.036596 KDa |
Recombinant expression | Organism: Escherichia coli MC1061 (bacteria) |
Sequence | String: GSSSQVQLVE SGGGLVQAGG SLRLSCAASG FPVGRHFMYW YRQAPGKERE WVAAIYSYGE YTEYADSVKG RFTISRDNAK NTVYLQMNS LKPEDTAVYY CYVYVGNEYW GQGTQVTVSA GRAGEQKLIS EEDLNSAVDH HHHHH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 67.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |