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Open data
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Basic information
Entry | Database: PDB / ID: 5gky | |||||||||
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Title | Structure of RyR1 in a closed state (C1 conformer) | |||||||||
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![]() | TRANSPORT PROTEIN/ISOMERASE / channel / ![]() | |||||||||
Function / homology | ![]() cytoplasmic side of membrane / ATP-gated ion channel activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bai, X.C. / Yan, Z. / Wu, J.P. / Yan, N. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The Central domain of RyR1 is the transducer for long-range allosteric gating of channel opening. Authors: Xiao-Chen Bai / Zhen Yan / Jianping Wu / Zhangqiang Li / Nieng Yan / ![]() ![]() Abstract: The ryanodine receptors (RyRs) are intracellular calcium channels responsible for rapid release of Ca(2+) from the sarcoplasmic/endoplasmic reticulum (SR/ER) to the cytoplasm, which is essential for ...The ryanodine receptors (RyRs) are intracellular calcium channels responsible for rapid release of Ca(2+) from the sarcoplasmic/endoplasmic reticulum (SR/ER) to the cytoplasm, which is essential for the excitation-contraction (E-C) coupling of cardiac and skeletal muscles. The near-atomic resolution structure of closed RyR1 revealed the molecular details of this colossal channel, while the long-range allosteric gating mechanism awaits elucidation. Here, we report the cryo-EM structures of rabbit RyR1 in three closed conformations at about 4 Å resolution and an open state at 5.7 Å. Comparison of the closed RyR1 structures shows a breathing motion of the cytoplasmic platform, while the channel domain and its contiguous Central domain remain nearly unchanged. Comparison of the open and closed structures shows a dilation of the S6 tetrahelical bundle at the cytoplasmic gate that leads to channel opening. During the pore opening, the cytoplasmic "O-ring" motif of the channel domain and the U-motif of the Central domain exhibit coupled motion, while the Central domain undergoes domain-wise displacement. These structural analyses provide important insight into the E-C coupling in skeletal muscles and identify the Central domain as the transducer that couples the conformational changes of the cytoplasmic platform to the gating of the central pore. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.8 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 9518MC ![]() 9519C ![]() 9520C ![]() 9521C ![]() 5gkzC ![]() 5gl0C ![]() 5gl1C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | ![]() Mass: 565908.625 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #2: Protein | Mass: 11967.705 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-ZN / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
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Molecular weight | Value: 2.2 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: ![]() ![]() ![]() ![]() | ||||||||||||||||||||||||
Buffer solution | pH: 7.4 Details: 20 mM MOPS-Na, pH 7.4, 250 mM NaCl, 2 mM DTT, 0.015% Tween20 (w/v) (Sigma-Aldrich) and protease inhibitor cocktail including 2 mM PMSF, 2.6 ug/ml aprotinin, 1.4 ug/ml pepstatin, and 10 ug/ml leupeptin (Amresco) | ||||||||||||||||||||||||
Specimen | Conc.: 0.066 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 | ||||||||||||||||||||||||
Vitrification![]() | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
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Processing
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Image processing | Details: Actually we use a prototype FEI Falcon-III detector | ||||||||||||||||||||||||||||
CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() ![]() | ||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119000 / Symmetry type: POINT |