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Yorodumi- EMDB-2807: Single-particle electron cryo-microscopy structure of ryanodine r... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2807 | |||||||||
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Title | Single-particle electron cryo-microscopy structure of ryanodine receptor RyR1 in complex with FKBP12 | |||||||||
Map data | Reconstruction of RyR1 | |||||||||
Sample |
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Keywords | ryanodine receptors / intracellular Ca2+ channel / in complex with its modulator FKBP12 / excitation-contraction coupling. | |||||||||
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 / smooth endoplasmic reticulum / voltage-gated calcium channel activity / skeletal muscle fiber development / striated muscle contraction / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / muscle contraction / release of sequestered calcium ion into cytosol / 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: 3.8 Å | |||||||||
Authors | Yan Z / Bai XC / Yan CY / Wu JP / Scheres S / Shi YG / Yan N | |||||||||
Citation | Journal: Nature / Year: 2015 Title: Structure of the rabbit ryanodine receptor RyR1 at near-atomic resolution. Authors: Zhen Yan / Xiaochen Bai / Chuangye Yan / Jianping Wu / Zhangqiang Li / Tian Xie / Wei Peng / Changcheng Yin / Xueming Li / Sjors H W Scheres / Yigong Shi / Nieng Yan / Abstract: The ryanodine receptors (RyRs) are high-conductance intracellular Ca(2+) channels that play a pivotal role in the excitation-contraction coupling of skeletal and cardiac muscles. RyRs are the largest ...The ryanodine receptors (RyRs) are high-conductance intracellular Ca(2+) channels that play a pivotal role in the excitation-contraction coupling of skeletal and cardiac muscles. RyRs are the largest known ion channels, with a homotetrameric organization and approximately 5,000 residues in each protomer. Here we report the structure of the rabbit RyR1 in complex with its modulator FKBP12 at an overall resolution of 3.8 Å, determined by single-particle electron cryomicroscopy. Three previously uncharacterized domains, named central, handle and helical domains, display the armadillo repeat fold. These domains, together with the amino-terminal domain, constitute a network of superhelical scaffold for binding and propagation of conformational changes. The channel domain exhibits the voltage-gated ion channel superfamily fold with distinct features. A negative-charge-enriched hairpin loop connecting S5 and the pore helix is positioned above the entrance to the selectivity-filter vestibule. The four elongated S6 segments form a right-handed helical bundle that closes the pore at the cytoplasmic border of the membrane. Allosteric regulation of the pore by the cytoplasmic domains is mediated through extensive interactions between the central domains and the channel domain. These structural features explain high ion conductance by RyRs and the long-range allosteric regulation of channel activities. | |||||||||
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_2807.map.gz | 166.5 MB | EMDB map data format | |
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Header (meta data) | emd-2807-v30.xml emd-2807.xml | 10 KB 10 KB | Display Display | EMDB header |
Images | RyR1.jpg | 103.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2807 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2807 | HTTPS FTP |
-Validation report
Summary document | emd_2807_validation.pdf.gz | 390 KB | Display | EMDB validaton report |
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Full document | emd_2807_full_validation.pdf.gz | 389.5 KB | Display | |
Data in XML | emd_2807_validation.xml.gz | 6.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2807 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2807 | HTTPS FTP |
-Related structure data
Related structure data | 3j8hMC 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_2807.map.gz / Format: CCP4 / Size: 173.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of RyR1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : rabbit RyR1 in complex with its modulator FKBP12
Entire | Name: rabbit RyR1 in complex with its modulator FKBP12 |
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Components |
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-Supramolecule #1000: rabbit RyR1 in complex with its modulator FKBP12
Supramolecule | Name: rabbit RyR1 in complex with its modulator FKBP12 / type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: 4 / Number unique components: 1 |
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Molecular weight | Experimental: 5.5 MDa / Theoretical: 5.5 MDa / Method: sequence |
-Macromolecule #1: ryanodine receptor RyR1
Macromolecule | Name: ryanodine receptor RyR1 / type: protein_or_peptide / ID: 1 / Details: The RyR1 is in complex with its modulator FKBP12 / Number of copies: 4 / Oligomeric state: tetramer / Recombinant expression: No |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit |
Molecular weight | Theoretical: 5.5 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.6 mg/mL |
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Buffer | pH: 8 / Details: 25 mM Tris-HCl, 150 mM NaCl, 2 mM DTT |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK III Method: Aliquots of 3uL of purified RYR1 at a concentration of approximately 30 nM were placed on glow-discharged holey carbon grids (Quantifoil CuR2/2), on which a home-made continuous carbon film ...Method: Aliquots of 3uL of purified RYR1 at a concentration of approximately 30 nM were placed on glow-discharged holey carbon grids (Quantifoil CuR2/2), on which a home-made continuous carbon film had previously been deposited. Grids were blotted for 2 s and flash frozen in liquid ethane using an FEI Vitrobot. |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 80 K / Max: 90 K / Average: 85 K |
Date | Jun 21, 2014 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Sampling interval: 14 µm / Number real images: 1500 / Average electron dose: 40 e/Å2 Details: An in-house built system was used to intercept the videos from the detector at a rate of 17 frames for the 1 s exposures. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 104748 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 5.6 µm / Nominal defocus min: 1.9 µm / Nominal magnification: 78000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | The 20 frames of each video were aligned using the whole-image motion correction method. We used the particles picking tool in the RELION for automated selection of particles. |
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CTF correction | Details: Each particle |
Final reconstruction | Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: OTHER / Software - Name: CTFFIND3, RELION Details: Use a newly developed statistical movie processing approach to compensate for beam-induced movement. Number images used: 65872 |