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Yorodumi- EMDB-10640: Rabbit ryanodine receptor 1 in the presence of 1mM Calcium in nat... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10640 | |||||||||
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Title | Rabbit ryanodine receptor 1 in the presence of 1mM Calcium in native membrane | |||||||||
Map data | Structure of rabbit ryanodine receptor 1 in the presence of 1mM Calcium in native membrane | |||||||||
Sample |
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Biological species | Oryctolagus cuniculus (rabbit) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 27.7 Å | |||||||||
Authors | Chen W / Kudryashev M | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: EMBO Rep / Year: 2020 Title: Structure of RyR1 in native membranes. Authors: Wenbo Chen / Mikhail Kudryashev / Abstract: Ryanodine receptor 1 (RyR1) mediates excitation-contraction coupling by releasing Ca from sarcoplasmic reticulum (SR) to the cytoplasm of skeletal muscle cells. RyR1 activation is regulated by ...Ryanodine receptor 1 (RyR1) mediates excitation-contraction coupling by releasing Ca from sarcoplasmic reticulum (SR) to the cytoplasm of skeletal muscle cells. RyR1 activation is regulated by several proteins from both the cytoplasm and lumen of the SR. Here, we report the structure of RyR1 from native SR membranes in closed and open states. Compared to the previously reported structures of purified RyR1, our structure reveals helix-like densities traversing the bilayer approximately 5 nm from the RyR1 transmembrane domain and sarcoplasmic extensions linking RyR1 to a putative calsequestrin network. We document the primary conformation of RyR1 in situ and its structural variations. The activation of RyR1 is associated with changes in membrane curvature and movement in the sarcoplasmic extensions. Our results provide structural insight into the mechanism of RyR1 in its native environment. | |||||||||
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_10640.map.gz | 3.6 MB | EMDB map data format | |
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Header (meta data) | emd-10640-v30.xml emd-10640.xml | 13.9 KB 13.9 KB | Display Display | EMDB header |
Images | emd_10640.png | 117 KB | ||
Masks | emd_10640_msk_1.map | 3.8 MB | Mask map | |
Others | emd_10640_half_map_1.map.gz emd_10640_half_map_2.map.gz | 3.6 MB 3.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10640 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10640 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10349 (Title: Cryo Electron Tomograms of Membrane Fractions of Rabbit Skeletal Muscle for Structural Determination of RyR1 in SR Vesicles Data size: 254.2 Data #1: 82 tilt series (frames aligned my motioncorr2) in .st stacks (mrc format for imod) including .tlt, .xf and .defocus files [tilt series]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10640.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of rabbit ryanodine receptor 1 in the presence of 1mM Calcium in native membrane | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.7 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_10640_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Structure of rabbit ryanodine receptor 1 in the...
File | emd_10640_half_map_1.map | ||||||||||||
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Annotation | Structure of rabbit ryanodine receptor 1 in the presence of 1mM Calcium in native membrane(half map 2) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Structure of rabbit ryanodine receptor 1 in the...
File | emd_10640_half_map_2.map | ||||||||||||
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Annotation | Structure of rabbit ryanodine receptor 1 in the presence of 1mM Calcium in native membrane (half map 1) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Rabbit ryanodine receptor 1 in the presence of 1mM Calcium in nat...
Entire | Name: Rabbit ryanodine receptor 1 in the presence of 1mM Calcium in native membrane |
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Components |
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-Supramolecule #1: Rabbit ryanodine receptor 1 in the presence of 1mM Calcium in nat...
Supramolecule | Name: Rabbit ryanodine receptor 1 in the presence of 1mM Calcium in native membrane type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle / Organelle: sarcoplasmic reticulum |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | tissue |
-Sample preparation
Buffer | pH: 7.1 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Extraction | Number tomograms: 9 / Number images used: 301 / Software: (Name: IMOD, Dynamo) |
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CTF correction | Software - Name: Gctf |
Final 3D classification | Software - Name: Dynamo |
Final angle assignment | Type: OTHER / Software - Name: Dynamo / Details: subtomogram alignment using Dynamo |
Final reconstruction | Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 27.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 9 |