+Open data
-Basic information
Entry | Database: PDB / ID: 5gky | |||||||||
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Title | Structure of RyR1 in a closed state (C1 conformer) | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN/ISOMERASE / channel / membrane protein / TRANSPORT PROTEIN-ISOMERASE complex | |||||||||
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 / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Bai, X.C. / Yan, Z. / Wu, J.P. / Yan, N. | |||||||||
Funding support | China, 2items
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Citation | Journal: Cell Res / Year: 2016 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5gky.cif.gz | 2.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5gky.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5gky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gky_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5gky_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5gky_validation.xml.gz | 385.3 KB | Display | |
Data in CIF | 5gky_validation.cif.gz | 593.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/5gky ftp://data.pdbj.org/pub/pdb/validation_reports/gk/5gky | HTTPS FTP |
-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 (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 565908.625 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P11716 #2: Protein | Mass: 11967.705 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: FKBP12 / Production host: Escherichia coli (E. coli) / References: UniProt: P62943, peptidylprolyl isomerase #3: Chemical | ChemComp-ZN / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Value: 2.2 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) / Plasmid: unknown | ||||||||||||||||||||||||
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: NO / Vitrification applied: YES | ||||||||||||||||||||||||
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 |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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) |
-Processing
EM software |
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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: C4 (4 fold cyclic) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119000 / Symmetry type: POINT |