|Entry||Database: EMDB / ID: EMD-10840|
|Title||Structure of RyR1 in apo/closed state in native membrane|
|Function / homology|
Function and homology information
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 / ossification involved in bone maturation / cellular response to caffeine / calcium-release channel activity / skin development ...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 / ossification involved in bone maturation / cellular response to caffeine / calcium-release channel activity / skin development / outflow tract morphogenesis / voltage-gated calcium channel activity / skeletal muscle fiber development / release of sequestered calcium ion into cytosol / toxic substance binding / cellular response to calcium ion / calcium ion transmembrane transport / calcium channel activity / sarcoplasmic reticulum membrane / sarcoplasmic reticulum / muscle contraction / disordered domain specific binding / drug binding / ion channel binding / protein homotetramerization / calmodulin binding / calcium ion binding / membrane / integral component of membrane / ATP binding / identical protein binding
MIR motif / Ryanodine receptor, SPRY domain 2 / RIH domain / B30.2/SPRY domain / Ryanodine receptor 1 / Ryanodine receptor Ryr / Ryanodine receptor, SPRY domain 1 / SPRY domain / Ion transport domain / Ryanodine receptor, SPRY domain 3 ...MIR motif / Ryanodine receptor, SPRY domain 2 / RIH domain / B30.2/SPRY domain / Ryanodine receptor 1 / Ryanodine receptor Ryr / Ryanodine receptor, SPRY domain 1 / SPRY domain / Ion transport domain / Ryanodine receptor, SPRY domain 3 / 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 / Mir domain superfamily / B30.2/SPRY domain superfamily / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor
Ryanodine receptor 1
|Biological species||Oryctolagus cuniculus (rabbit)|
|Method||subtomogram averaging / cryo EM / Resolution: 9.1 Å|
|Authors||Chen W / Sanchez R / Zhang Y / Dietrich L / Kudryashev M|
|Funding support|| Germany, 1 items |
|Citation||Journal: Nat Commun / Year: 2020|
Title: Subnanometer-resolution structure determination in situ by hybrid subtomogram averaging - single particle cryo-EM.
Authors: Ricardo M Sanchez / Yingyi Zhang / Wenbo Chen / Lea Dietrich / Mikhail Kudryashev /
Abstract: Cryo-electron tomography combined with subtomogram averaging (StA) has yielded high-resolution structures of macromolecules in their native context. However, high-resolution StA is not commonplace ...Cryo-electron tomography combined with subtomogram averaging (StA) has yielded high-resolution structures of macromolecules in their native context. However, high-resolution StA is not commonplace due to beam-induced sample drift, images with poor signal-to-noise ratios (SNR), challenges in CTF correction, and limited particle number. Here we address these issues by collecting tilt series with a higher electron dose at the zero-degree tilt. Particles of interest are then located within reconstructed tomograms, processed by conventional StA, and then re-extracted from the high-dose images in 2D. Single particle analysis tools are then applied to refine the 2D particle alignment and generate a reconstruction. Use of our hybrid StA (hStA) workflow improved the resolution for tobacco mosaic virus from 7.2 to 4.4 Å and for the ion channel RyR1 in crowded native membranes from 12.9 to 9.1 Å. These resolution gains make hStA a promising approach for other StA projects aimed at achieving subnanometer resolution.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_10840.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.7 Å|
|Symmetry||Space group: 1|
CCP4 map header:
|Projections & Slices|
-Half map: half map 1 of structure of RyR1 in...
|Annotation||half map 1 of structure of RyR1 in native membrane in apo/closed state|
|Projections & Slices|
-Half map: half map 2 of structure of RyR1 in...
-Entire Sarcoplasmic reticulum
|Entire||Name: Sarcoplasmic reticulum / Number of components: 1|
-Component #1: cellular-component, Sarcoplasmic reticulum
|Cellular-component||Name: Sarcoplasmic reticulum / Recombinant expression: No|
|Source||Species: Oryctolagus cuniculus (rabbit)|
|Specimen||Specimen state: Tissue / Method: cryo EM|
|Sample solution||pH: 7.1|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Processing||Method: subtomogram averaging / Applied symmetry: C4 (4 fold cyclic) / Number of subtomograms: 2563|
|3D reconstruction||Resolution: 9.1 Å / Resolution method: FSC 0.143 CUT-OFF|
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