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Yorodumi- PDB-7k0s: Cryo-EM structure of rabbit RyR1 in the presence of Mg2+ and AMP-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7k0s | |||||||||||||||||||||
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Title | Cryo-EM structure of rabbit RyR1 in the presence of Mg2+ and AMP-PCP in nanodisc | |||||||||||||||||||||
Components | RyR1 | |||||||||||||||||||||
Keywords | TRANSPORT PROTEIN / Ryanodine Receptor / RyR1 / Intracellular Calcium channel / Mg2+ / Inhibition / Excitation-Contraction coupling | |||||||||||||||||||||
Function / homology | PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER Function and homology information | |||||||||||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||||||||||||||
Authors | Nayak, A.R. / Samso, M. | |||||||||||||||||||||
Funding support | United States, 6items
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Citation | Journal: Nat Commun / Year: 2024 Title: Interplay between Mg2+ and Ca2+ at multiple sites of the ryanodine receptor Authors: Nayak, A.R. / Rangubpit, W. / Will, A.H. / Hu, Y. / Castro-Hartmann, P. / Lobo, J.J. / Dryden, K. / Lamb, G.D. / Sompornpisut, P. / Samso, M. | |||||||||||||||||||||
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 | 7k0s.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7k0s.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7k0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7k0s_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7k0s_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7k0s_validation.xml.gz | 345 KB | Display | |
Data in CIF | 7k0s_validation.cif.gz | 568.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/7k0s ftp://data.pdbj.org/pub/pdb/validation_reports/k0/7k0s | HTTPS FTP |
-Related structure data
Related structure data | 22615MC 7umzC 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: 533663.250 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Organ: Skeletal muscle / Strain: New Zealand White #2: Chemical | ChemComp-ACP / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-MG / Has ligand of interest | Y | |
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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: Rabbit RyR1 with Mg2+ and AMP-PCP / Type: COMPLEX Details: Purified RyR1 was reconstituted with membrane scaffold protein MSP1E3D1, and POPC. Entity ID: #1 / Source: NATURAL | |||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 2.26 MDa / Experimental value: YES | |||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / Strain: New Zealand White / Cellular location: Sarcoplasmic Reticulum membrane / Organ: Skeletal Muscle / Organelle: Sarcoplasmic Reticulum | |||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 4.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Purified RyR1 was reconstituted with membrane scaffold protein MSP1E3D1, and POPC in 1:2:50 molar ratio. | |||||||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1 | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K Details: Sample was blotted for 1 second on both sides with Whatman hardened ashless filter paper with blot force 2. |
-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 magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 3371 |
EM imaging optics | Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 60 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 115741 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68155 / Num. of class averages: 2 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |