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Yorodumi- PDB-8drp: Focus/local refined map in C4 of signal subtracted RyR1 particles -
+Open data
-Basic information
Entry | Database: PDB / ID: 8drp | |||||||||
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Title | Focus/local refined map in C4 of signal subtracted RyR1 particles | |||||||||
Components | Ryanodine receptor 1 | |||||||||
Keywords | MEMBRANE PROTEIN / Ryanodine receptor / Ion channel / Snake toxin / Calcin / Complex / TOXIN | |||||||||
Function / homology | Function and homology information 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 / cellular response to caffeine / outflow tract morphogenesis / intracellularly gated calcium channel activity ...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 / cellular response to caffeine / outflow tract morphogenesis / intracellularly gated calcium channel activity / organelle membrane / toxic substance binding / smooth endoplasmic reticulum / voltage-gated calcium channel activity / skeletal muscle fiber development / striated muscle contraction / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / cellular response to calcium ion / sarcoplasmic reticulum / muscle contraction / 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 / calcium ion binding / ATP binding / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å | |||||||||
Authors | Haji-Ghassemi, O. / Van Petegm, F. | |||||||||
Funding support | Canada, 2items
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Citation | Journal: Sci Adv / Year: 2023 Title: Cryo-EM analysis of scorpion toxin binding to Ryanodine Receptors reveals subconductance that is abolished by PKA phosphorylation. Authors: Omid Haji-Ghassemi / Yu Seby Chen / Kellie Woll / Georgina B Gurrola / Carmen R Valdivia / Wenxuan Cai / Songhua Li / Hector H Valdivia / Filip Van Petegem / Abstract: Calcins are peptides from scorpion venom with the unique ability to cross cell membranes, gaining access to intracellular targets. Ryanodine Receptors (RyR) are intracellular ion channels that ...Calcins are peptides from scorpion venom with the unique ability to cross cell membranes, gaining access to intracellular targets. Ryanodine Receptors (RyR) are intracellular ion channels that control release of Ca from the endoplasmic and sarcoplasmic reticulum. Calcins target RyRs and induce long-lived subconductance states, whereby single-channel currents are decreased. We used cryo-electron microscopy to reveal the binding and structural effects of imperacalcin, showing that it opens the channel pore and causes large asymmetry throughout the cytosolic assembly of the tetrameric RyR. This also creates multiple extended ion conduction pathways beyond the transmembrane region, resulting in subconductance. Phosphorylation of imperacalcin by protein kinase A prevents its binding to RyR through direct steric hindrance, showing how posttranslational modifications made by the host organism can determine the fate of a natural toxin. The structure provides a direct template for developing calcin analogs that result in full channel block, with potential to treat RyR-related disorders. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8drp.cif.gz | 690.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8drp.ent.gz | 391.6 KB | Display | PDB format |
PDBx/mmJSON format | 8drp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8drp_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8drp_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8drp_validation.xml.gz | 75.6 KB | Display | |
Data in CIF | 8drp_validation.cif.gz | 108.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/8drp ftp://data.pdbj.org/pub/pdb/validation_reports/dr/8drp | HTTPS FTP |
-Related structure data
Related structure data | 27680MC 8dtbC 8dujC 8dveC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: Chemical | ChemComp-CFF / #3: Chemical | ChemComp-ATP / #4: Chemical | ChemComp-ZN / Has ligand of interest | N | |
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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: Ryanodine Receptor 1 / Type: COMPLEX / Details: Rabbit skeletal muscle Ryanodine Receptor 1 / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Value: 2.2 MDa / Experimental value: YES |
Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7277 |
Image scans | Width: 4096 / Height: 4096 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 335577 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL |