|Entry||Database: EMDB / ID: 4295|
|Title||Structure of Ryanodine Receptor 1 in nanodiscs in the presence of calcium and ATP|
|Sample||Ryanodine receptor 1 in nanodiscs in presence of calcium and ATP:|
Ryanodine receptor 1 / ligand
|Function / homology||RIH domain / B30.2/SPRY domain / Ryanodine receptor, SPRY domain 2 / Ryanodine receptor, SPRY domain 3 / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor 1 / MIR motif / Ryanodine receptor-related / EF-hand domain / Inositol 1,4,5-trisphosphate/ryanodine receptor ...RIH domain / B30.2/SPRY domain / Ryanodine receptor, SPRY domain 2 / Ryanodine receptor, SPRY domain 3 / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor 1 / MIR motif / Ryanodine receptor-related / EF-hand domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / Ryanodine receptor Ryr / SPRY domain / Ion transport domain / Ryanodine Receptor TM 4-6 / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily / Ryanodine receptor / RyR/IP3 receptor binding core, RIH domain superfamily / RyR/IP3R Homology associated domain / Mir domain superfamily / RyR and IP3R Homology associated / Ion transport protein / SPRY domain / RIH domain / RyR domain / MIR domain / MIR domain profile. / B30.2/SPRY domain profile. / EF-hand domain pair / Inositol 1,4,5-trisphosphate/ryanodine receptor / Ryanodine Receptor TM 4-6 / integral component of organelle membrane / ATP-gated ion channel activity / ryanodine-sensitive calcium-release channel activity / terminal cisterna / ryanodine receptor complex / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cellular response to caffeine / ossification involved in bone maturation / calcium-release channel activity / skin development / voltage-gated calcium channel activity / outflow tract morphogenesis / sarcoplasmic reticulum membrane / release of sequestered calcium ion into cytosol / skeletal muscle fiber development / sarcoplasmic reticulum / toxic substance binding / calcium channel activity / calcium ion transmembrane transport / muscle contraction / cellular response to calcium ion / protein homotetramerization / disordered domain specific binding / drug binding / ion channel binding / calmodulin binding / calcium ion binding / membrane / integral component of membrane / ATP binding / identical protein binding / Ryanodine receptor 1|
Function and homology information
|Source||Oryctolagus cuniculus (rabbit) / Rabbit (rabbit)|
|Method||single particle reconstruction / cryo EM / 8.2 Å resolution|
|Authors||Willegems K / Efremov RG|
|Citation||Journal: Structure / Year: 2018|
Title: Influence of Lipid Mimetics on Gating of Ryanodine Receptor.
Authors: Katrien Willegems / Rouslan G Efremov
Abstract: Understanding gating principles of ion channels at high resolution is of great importance. Here we investigate the conformational transition from closed to open state in ryanodine receptor 1 (RyR1) ...Understanding gating principles of ion channels at high resolution is of great importance. Here we investigate the conformational transition from closed to open state in ryanodine receptor 1 (RyR1) reconstituted into lipid nanodiscs. RyR1 is a homotetrameric giant ion channel that couples excitation of muscle cells to fast calcium release from the sarcoplasmic reticulum. Using single-particle cryo-EM we show that RyR1 reconstituted into lipid nanodiscs is stabilized in the open conformation when bound to the plant toxin ryanodine, but not in the presence of its physiological activators, calcium and ATP. Further, using ryanodine binding assays we show that membrane mimetics influence RyR1 transition between closed and open-channel conformations. We find that all detergents, including fluorinated detergents added to nanodiscs, stabilize closed state of RyR1. Our biochemical results correlate with available structural data and suggest optimal conditions for structural studies of RyR1 gating.
|Validation Report||PDB-ID: 6foo|
SummaryFull reportAbout validation report
|Date||Deposition: Feb 8, 2018 / Header (metadata) release: May 9, 2018 / Map release: Aug 8, 2018 / Last update: Nov 28, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_4295.map.gz (map file in CCP4 format, 186625 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.645 Å|
CCP4 map header:
-Entire Ryanodine receptor 1 in nanodiscs in presence of calcium and ATP
|Entire||Name: Ryanodine receptor 1 in nanodiscs in presence of calcium and ATP|
Number of components: 3
-Component #1: protein, Ryanodine receptor 1 in nanodiscs in presence of calcium...
|Protein||Name: Ryanodine receptor 1 in nanodiscs in presence of calcium and ATP|
Recombinant expression: No
|Mass||Theoretical: 2.2 MDa|
|Source||Species: Oryctolagus cuniculus (rabbit) / Strain: New Zealand white rabbit|
-Component #2: protein, Ryanodine receptor 1
|Protein||Name: Ryanodine receptor 1 / Number of Copies: 4 / Recombinant expression: No|
|Mass||Theoretical: 532.709688 kDa|
|Source||Species: Rabbit (rabbit)|
|Source (natural)||Organ or tissue: skeletal muscle|
-Component #3: ligand, ZINC ION
|Ligand||Name: ZINC ION / Number of Copies: 4 / Recombinant expression: No|
|Mass||Theoretical: 6.540905 MDa|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Specimen conc.: 3 mg/ml / pH: 7.4|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 293.15 K|
-Electron microscopy imaging
Model: Talos Arctica / Image courtesy: FEI Company
|Imaging||Microscope: FEI TALOS ARCTICA|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1.7 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 92000.0 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 2000.0 - 3000.0 nm|
|Specimen Holder||Model: OTHER|
|Camera||Detector: FEI FALCON II (4k x 4k)|
|Image acquisition||Number of digital images: 1906 / Sampling size: 14 microns|
|Processing||Method: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 42500|
|3D reconstruction||Software: RELION / Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF|
-Atomic model buiding
|Modeling #1||Refinement space: REAL|
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