|Entry||Database: PDB / ID: 6foo|
|Title||Structure of Ryanodine Receptor 1 in nanodiscs in the presence of calcium and ATP|
|Components||Ryanodine receptor 1|
|Keywords||MEMBRANE PROTEIN / calcium release channel / nanodiscs|
|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 / Inositol 1,4,5-trisphosphate/ryanodine receptor / Ryanodine Receptor TM 4-6 / EF-hand domain pair / B30.2/SPRY domain profile. / MIR domain profile. / MIR domain / RyR domain / RIH domain / SPRY domain / Ion transport protein / RyR and IP3R Homology associated / integral component of organelle membrane / ATP-gated ion channel activity / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / terminal cisterna / ryanodine receptor complex / 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 / calcium channel activity / sarcoplasmic reticulum / calcium ion transmembrane transport / toxic substance binding / 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
|Specimen source||Oryctolagus cuniculus (rabbit)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 8.2 Å resolution|
|Authors||Willegems, K. / Efremov, R.G.|
|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.
SummaryFull reportAbout validation report
|Date||Deposition: Feb 8, 2018 / Release: Aug 8, 2018|
|Structure viewer||Molecule: |
Downloads & links
A: Ryanodine receptor 1
B: Ryanodine receptor 1
C: Ryanodine receptor 1
D: Ryanodine receptor 1
Mass: 532225.562 Da / Num. of mol.: 4 / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle / Strain: New Zealand White rabbit / References: UniProt: P11716
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: single particle reconstruction|
|Component||Name: Ryanodine receptor 1 in nanodiscs in presence of calcium and ATP|
Type: COMPLEX / Entity ID: 1 / Source: NATURAL
|Molecular weight||Value: 2.2 MDa / Experimental value: NO|
|Source (natural)||Cellular location: sarcoplasmic reticulum / Organism: Oryctolagus cuniculus (rabbit) / Strain: New Zealand white rabbit / Tissue: skeletal muscle|
|Buffer solution||pH: 7.4|
|Specimen||Conc.: 3 mg/ml / Details: Protein was reconstituted into lipid nanodiscs / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Grid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil R2/1|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Chamber temperature: 293.15 kelvins|
-Electron microscopy imaging
Model: Talos Arctica / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TALOS ARCTICA|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 92000 / Nominal defocus max: 3000 nm / Nominal defocus min: 2000 nm|
|Specimen holder||Cryogen: NITROGEN|
|Image recording||Electron dose: 1.7 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) / Number of grids imaged: 1 / Number of real images: 1906|
|Image scans||Sampling size: 14 microns / Width: 4096 / Height: 4096 / Movie frames/image: 16 / Used frames/image: 1-16|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Particle selection||Number of particles selected: 90000|
|Symmetry||Point symmetry: C4|
|3D reconstruction||Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 42500 / Symmetry type: POINT|
|Atomic model building||Ref space: REAL|
|Refine||Stereochemistry target values: GeoStd + Monomer Library|
|Refine LS restraints|
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
-Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
+Apr 13, 2016. Omokage search got faster
Omokage search got faster
- The computation time became ~1/2 compared to the previous version by re-optimization of data accession
- Enjoy "shape similarity" of biomolecules, more!
Related info.: Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi