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Yorodumi- EMDB-2751: Structure of the ryanodine receptor at resolution of 6.1 A in clo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2751 | |||||||||
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Title | Structure of the ryanodine receptor at resolution of 6.1 A in closed state | |||||||||
Map data | reconstruction of rye reconstituted in lipid nanodiscs in closed state | |||||||||
Sample |
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Keywords | calcium binding / ion channel / muscular contraction / conformational changes. | |||||||||
Function / homology | Function and homology information 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 ...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 / toxic substance binding / smooth endoplasmic reticulum / voltage-gated calcium channel activity / skeletal muscle fiber development / striated muscle contraction / muscle contraction / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / cellular response to calcium ion / sarcoplasmic reticulum / 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 / calcium ion binding / ATP binding / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.1 Å | |||||||||
Authors | Efremov RG / Leitner A / Aebersold R / Raunser S | |||||||||
Citation | Journal: Nature / Year: 2015 Title: Architecture and conformational switch mechanism of the ryanodine receptor. Authors: Rouslan G Efremov / Alexander Leitner / Ruedi Aebersold / Stefan Raunser / Abstract: Muscle contraction is initiated by the release of calcium (Ca(2+)) from the sarcoplasmic reticulum into the cytoplasm of myocytes through ryanodine receptors (RyRs). RyRs are homotetrameric channels ...Muscle contraction is initiated by the release of calcium (Ca(2+)) from the sarcoplasmic reticulum into the cytoplasm of myocytes through ryanodine receptors (RyRs). RyRs are homotetrameric channels with a molecular mass of more than 2.2 megadaltons that are regulated by several factors, including ions, small molecules and proteins. Numerous mutations in RyRs have been associated with human diseases. The molecular mechanism underlying the complex regulation of RyRs is poorly understood. Using electron cryomicroscopy, here we determine the architecture of rabbit RyR1 at a resolution of 6.1 Å. We show that the cytoplasmic moiety of RyR1 contains two large α-solenoid domains and several smaller domains, with folds suggestive of participation in protein-protein interactions. The transmembrane domain represents a chimaera of voltage-gated sodium and pH-activated ion channels. We identify the calcium-binding EF-hand domain and show that it functions as a conformational switch allosterically gating the channel. | |||||||||
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_2751.map.gz | 18.4 MB | EMDB map data format | |
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Header (meta data) | emd-2751-v30.xml emd-2751.xml | 13.1 KB 13.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_2751_fsc.xml | 12.2 KB | Display | FSC data file |
Images | 2751-map-snapshot.jpg | 67.2 KB | ||
Masks | emd_2751_msk_1.map | 216 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2751 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2751 | HTTPS FTP |
-Validation report
Summary document | emd_2751_validation.pdf.gz | 304.4 KB | Display | EMDB validaton report |
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Full document | emd_2751_full_validation.pdf.gz | 303.6 KB | Display | |
Data in XML | emd_2751_validation.xml.gz | 13.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2751 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2751 | HTTPS FTP |
-Related structure data
Related structure data | 4uwaMC 2752C 4uweC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2751.map.gz / Format: CCP4 / Size: 210.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | reconstruction of rye reconstituted in lipid nanodiscs in closed state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.42 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Segmentation: The mask used for calculating FSC
Annotation | The mask used for calculating FSC | ||||||||||||
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File | emd_2751_msk_1.map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ryanodine receptor 1 (calcium release channel) from rabbit
Entire | Name: Ryanodine receptor 1 (calcium release channel) from rabbit |
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Components |
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-Supramolecule #1000: Ryanodine receptor 1 (calcium release channel) from rabbit
Supramolecule | Name: Ryanodine receptor 1 (calcium release channel) from rabbit type: sample / ID: 1000 / Details: protein was reconstituted in lipid nanodiscs / Oligomeric state: tetramer / Number unique components: 1 |
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Molecular weight | Theoretical: 2.26 MDa |
-Macromolecule #1: Ryanodine receptor 1
Macromolecule | Name: Ryanodine receptor 1 / type: protein_or_peptide / ID: 1 / Name.synonym: Skeletal muscle calcium release channel / Number of copies: 4 / Oligomeric state: tetramer / Recombinant expression: No |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: muscle / Organelle: Sarcoplasmic reticulum / Location in cell: Sarcoplasmic reticulum membrane |
Molecular weight | Theoretical: 2.26 MDa |
Sequence | UniProtKB: Ryanodine receptor 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.4 Details: 10 mM MOPS, 200 mM NaCl, 1mM EGTA, 0.2% fluorinated octyl-maltoside |
Grid | Details: Quantifoil R 2/1 holey carbon grid |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER Method: protein solution was applied on glow discharged grid and blotted for 4 seconds before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Cs | 0 |
Temperature | Min: 80 K |
Date | Feb 3, 2014 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 2320 / Average electron dose: 20 e/Å2 Details: Images were collected automatically with CPU software and using movie mode with 7 frames per image. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.003 µm / Nominal defocus min: 0.001 µm / Nominal magnification: 47000 / Cs: mm |
Sample stage | Specimen holder: liquid nitorgen cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera |
Details | The domains with known crystal structures: 2AOX, 4ERT, 2R9R, or modelled with structure prediction programs were separately fitted in Chimera. The remaining domains were build ab initio in coot |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-4uwa: |
-Atomic model buiding 2
Initial model | PDB ID: |
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Software | Name: Chimera |
Details | The domains with known crystal structures: 2AOX, 4ERT, 2R9R, or modelled with structure prediction programs were separately fitted in Chimera. The remaining domains were build ab initio in coot |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-4uwa: |
-Atomic model buiding 3
Initial model | PDB ID: |
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Software | Name: Chimera |
Details | The domains with known crystal structures: 2AOX, 4ERT, 2R9R, or modelled with structure prediction programs were separately fitted in Chimera. The remaining domains were build ab initio in coot |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-4uwa: |