+Open data
-Basic information
Entry | Database: PDB / ID: 5ta3 | ||||||
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Title | Structure of rabbit RyR1 (Caffeine/ATP/Ca2+ dataset, class 2) | ||||||
Components |
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Keywords | TRANSPORT PROTEIN/ISOMERASE / RyR / Ca2+ / EC coupling / gating / TRANSPORT PROTEIN-ISOMERASE complex | ||||||
Function / homology | Function and homology information 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 / negative regulation of release of sequestered calcium ion into cytosol / terminal cisterna / neuronal action potential propagation / ryanodine receptor complex / insulin secretion involved in cellular response to glucose stimulus ...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 / negative regulation of release of sequestered calcium ion into cytosol / terminal cisterna / neuronal action potential propagation / ryanodine receptor complex / insulin secretion involved in cellular response to glucose stimulus / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to redox state / protein maturation by protein folding / ossification involved in bone maturation / 'de novo' protein folding / negative regulation of heart rate / skin development / FK506 binding / organelle membrane / positive regulation of axon regeneration / cellular response to caffeine / channel regulator activity / outflow tract morphogenesis / intracellularly gated calcium channel activity / smooth muscle contraction / response to vitamin E / toxic substance binding / voltage-gated calcium channel activity / smooth endoplasmic reticulum / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / skeletal muscle fiber development / striated muscle contraction / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / T cell proliferation / Ion homeostasis / release of sequestered calcium ion into cytosol / muscle contraction / regulation of cytosolic calcium ion concentration / calcium channel complex / sarcoplasmic reticulum membrane / cellular response to calcium ion / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium-mediated signaling / calcium ion transmembrane transport / 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 | Homo sapiens (human) Oryctolagus cuniculus (rabbit) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å | ||||||
Authors | Clarke, O.B. / des Georges, A. / Zalk, R. / Marks, A.R. / Hendrickson, W.A. / Frank, J. | ||||||
Citation | Journal: Cell / Year: 2016 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5ta3.cif.gz | 2.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5ta3.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5ta3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ta3_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 5ta3_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 5ta3_validation.xml.gz | 368.5 KB | Display | |
Data in CIF | 5ta3_validation.cif.gz | 594.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ta/5ta3 ftp://data.pdbj.org/pub/pdb/validation_reports/ta/5ta3 | HTTPS FTP |
-Related structure data
Related structure data | 8377MC 8342C 8372C 8373C 8374C 8375C 8376C 8378C 8379C 8380C 8381C 8382C 8383C 8384C 8385C 8386C 8387C 8388C 8389C 8390C 8391C 8392C 8393C 8394C 8395C 5t15C 5t9mC 5t9nC 5t9rC 5t9sC 5t9vC 5talC 5tamC 5tanC 5tapC 5taqC 5tasC 5tatC 5tauC 5tavC 5tawC 5taxC 5tayC 5tazC 5tb0C 5tb1C 5tb2C 5tb3C 5tb4C 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
-Protein , 2 types, 8 molecules FAHJBGIE
#1: Protein | Mass: 11798.501 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1B, FKBP12.6, FKBP1L, FKBP9, OTK4 / Production host: Escherichia coli (E. coli) / References: UniProt: P68106, peptidylprolyl isomerase #2: Protein | Mass: 475107.719 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Skeletal muscle / References: UniProt: P11716 |
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-Non-polymers , 4 types, 16 molecules
#3: Chemical | ChemComp-ATP / #4: Chemical | ChemComp-CFF / #5: Chemical | ChemComp-ZN / #6: Chemical | ChemComp-CA / |
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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
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 |
-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 |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.4 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 4.6 Angstrom. Symmetry type: POINT |