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Yorodumi- EMDB-47395: Structure of RyR1 in the open state in the presence of oxopyricid -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-47395 | |||||||||
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Title | Structure of RyR1 in the open state in the presence of oxopyricid | |||||||||
Map data | Structure of RyR1 in the open state in the presence of oxopyricid | |||||||||
Sample |
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Keywords | calcium channel / TRANSPORT PROTEIN / sarcoplasmic reticulum | |||||||||
Function / homology | Function and homology information cytoplasmic side of membrane / ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / organelle membrane / cellular response to caffeine ...cytoplasmic side of membrane / ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / organelle membrane / cellular response to caffeine / outflow tract morphogenesis / intracellularly gated calcium channel activity / regulation of ryanodine-sensitive calcium-release channel activity / toxic substance binding / voltage-gated calcium channel activity / smooth endoplasmic reticulum / skeletal muscle fiber development / striated muscle contraction / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / release of sequestered calcium ion into cytosol / muscle contraction / sarcoplasmic reticulum membrane / cellular response to calcium ion / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium ion transmembrane transport / calcium channel activity / sarcolemma / Z disc / intracellular calcium ion homeostasis / disordered domain specific binding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / intracellular membrane-bounded organelle / calcium ion binding / ATP binding / identical protein binding / membrane / cytosol Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Miotto MC / Marks AR | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: Targeting Ryanodine Receptors with Allopurinol and Xanthine Derivatives for the Treatment of Cardiac and Musculoskeletal Weakness Disorders Authors: Miotto MC | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_47395.map.gz | 253.5 MB | EMDB map data format | |
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Header (meta data) | emd-47395-v30.xml emd-47395.xml | 26.9 KB 26.9 KB | Display Display | EMDB header |
Images | emd_47395.png | 124.3 KB | ||
Filedesc metadata | emd-47395.cif.gz | 9.3 KB | ||
Others | emd_47395_additional_1.map.gz emd_47395_half_map_1.map.gz emd_47395_half_map_2.map.gz | 256.8 MB 474 MB 474 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-47395 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-47395 | HTTPS FTP |
-Validation report
Summary document | emd_47395_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_47395_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_47395_validation.xml.gz | 19 KB | Display | |
Data in CIF | emd_47395_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-47395 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-47395 | HTTPS FTP |
-Related structure data
Related structure data | 9e1iMC 9e17C 9e18C 9e19C 9e1aC 9e1bC 9e1cC 9e1dC 9e1eC 9e1fC 9e1gC 9e1hC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_47395.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Structure of RyR1 in the open state in the presence of oxopyricid | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8275 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Structure of RyR1 in the open state in...
File | emd_47395_additional_1.map | ||||||||||||
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Annotation | Structure of RyR1 in the open state in the presence of oxopyricid - focued map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_47395_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_47395_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Complex of RyR1 and Calstabin-1
+Supramolecule #1: Complex of RyR1 and Calstabin-1
+Supramolecule #2: Ryanodine Receptor 1
+Supramolecule #3: Calstabin-1
+Macromolecule #1: Ryanodine receptor 1
+Macromolecule #2: Peptidyl-prolyl cis-trans isomerase FKBP1A
+Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #4: CALCIUM ION
+Macromolecule #5: ZINC ION
+Macromolecule #6: oxopyricid
+Macromolecule #7: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL | |||||||||||||||||||||||||||
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Buffer | pH: 7.4 Component:
Details: 2 mM oxopyricid was added to the final sample from a 20 mM stock solution in buffer. | |||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Temperature | Min: 80.0 K / Max: 100.0 K |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average electron dose: 58.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL / In silico model: CryoSPARC ab initio |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 33308 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |