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Open data
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Basic information
Entry | Database: PDB / ID: 5tat | ||||||
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Title | Structure of rabbit RyR1 (Caffeine/ATP/EGTA dataset, class 2) | ||||||
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![]() | TRANSPORT PROTEIN/ISOMERASE / RyR / Ca2+ / EC coupling / gating / TRANSPORT PROTEIN-ISOMERASE complex | ||||||
Function / homology | ![]() ATP-gated ion channel activity / positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / terminal cisterna / ryanodine receptor complex / negative regulation of release of sequestered calcium ion into cytosol / ryanodine-sensitive calcium-release channel activity / neuronal action potential propagation ...ATP-gated ion channel activity / positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / terminal cisterna / ryanodine receptor complex / negative regulation of release of sequestered calcium ion into cytosol / ryanodine-sensitive calcium-release channel activity / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / response to redox state / protein maturation by protein folding / 'de novo' protein folding / skin development / negative regulation of heart rate / organelle membrane / FK506 binding / positive regulation of axon regeneration / cellular response to caffeine / outflow tract morphogenesis / channel regulator activity / intracellularly gated calcium channel activity / smooth muscle contraction / toxic substance binding / smooth endoplasmic reticulum / response to vitamin E / voltage-gated calcium channel activity / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / skeletal muscle fiber development / striated muscle contraction / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / muscle contraction / T cell proliferation / release of sequestered calcium ion into cytosol / Ion homeostasis / regulation of cytosolic calcium ion concentration / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to calcium ion / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium ion transmembrane transport / calcium-mediated signaling / response to hydrogen peroxide / calcium channel activity / Stimuli-sensing channels / sarcolemma / Z disc / intracellular calcium ion homeostasis / disordered domain specific binding / positive regulation of cytosolic calcium ion concentration / protein refolding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / signaling receptor binding / calcium ion binding / ATP binding / identical protein binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å | ||||||
![]() | Clarke, O.B. / des Georges, A. / Zalk, R. / Marks, A.R. / Hendrickson, W.A. / Frank, J. | ||||||
![]() | ![]() Title: Structural Basis for Gating and Activation of RyR1. Authors: Amédée des Georges / Oliver B Clarke / Ran Zalk / Qi Yuan / Kendall J Condon / Robert A Grassucci / Wayne A Hendrickson / Andrew R Marks / Joachim Frank / ![]() Abstract: The type-1 ryanodine receptor (RyR1) is an intracellular calcium (Ca(2+)) release channel required for skeletal muscle contraction. Here, we present cryo-EM reconstructions of RyR1 in multiple ...The type-1 ryanodine receptor (RyR1) is an intracellular calcium (Ca(2+)) release channel required for skeletal muscle contraction. Here, we present cryo-EM reconstructions of RyR1 in multiple functional states revealing the structural basis of channel gating and ligand-dependent activation. Binding sites for the channel activators Ca(2+), ATP, and caffeine were identified at interdomain interfaces of the C-terminal domain. Either ATP or Ca(2+) alone induces conformational changes in the cytoplasmic assembly ("priming"), without pore dilation. In contrast, in the presence of all three activating ligands, high-resolution reconstructions of open and closed states of RyR1 were obtained from the same sample, enabling analyses of conformational changes associated with gating. Gating involves global conformational changes in the cytosolic assembly accompanied by local changes in the transmembrane domain, which include bending of the S6 transmembrane segment and consequent pore dilation, displacement, and deformation of the S4-S5 linker and conformational changes in the pseudo-voltage-sensor domain. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.7 MB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8384MC ![]() 8342C ![]() 8372C ![]() 8373C ![]() 8374C ![]() 8375C ![]() 8376C ![]() 8377C ![]() 8378C ![]() 8379C ![]() 8380C ![]() 8381C ![]() 8382C ![]() 8383C ![]() 8385C ![]() 8386C ![]() 8387C ![]() 8388C ![]() 8389C ![]() 8390C ![]() 8391C ![]() 8392C ![]() 8393C ![]() 8394C ![]() 8395C ![]() 5t15C ![]() 5t9mC ![]() 5t9nC ![]() 5t9rC ![]() 5t9sC ![]() 5t9vC ![]() 5ta3C ![]() 5talC ![]() 5tamC ![]() 5tanC ![]() 5tapC ![]() 5taqC ![]() 5tasC ![]() 5tauC ![]() 5tavC ![]() 5tawC ![]() 5taxC ![]() 5tayC ![]() 5tazC ![]() 5tb0C ![]() 5tb1C ![]() 5tb2C ![]() 5tb3C ![]() 5tb4C 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: 11798.501 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 475107.719 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Chemical | ChemComp-ATP / #4: Chemical | ChemComp-CFF / #5: 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 |
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Sample preparation
Component | Name: RyR1-Cs2 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES |
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Buffer solution | pH: 7.4 |
Specimen | Conc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K Details: Blotted for 3-4 seconds on both sides with Whatman ashless filter paper, blot force 3, wait time 30 seconds |
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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 |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55564 / Algorithm: FOURIER SPACE Details: The reported resolution is for the core. The resolution of the whole assembly is 5.3 Angstrom. Symmetry type: POINT |