[English] 日本語
Yorodumi- PDB-7k0t: Cryo-EM structure of rabbit RyR1 in the presence of AMP-PCP in na... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7k0t | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of rabbit RyR1 in the presence of AMP-PCP in nanodisc | |||||||||||||||||||||
Components | RyR1 | |||||||||||||||||||||
Keywords | TRANSPORT PROTEIN / Ryanodine Receptor / RyR1 / Intracellular Calcium channel / Excitation-Contraction coupling / ATP | |||||||||||||||||||||
Function / homology | PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER Function and homology information | |||||||||||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||||||||||||||
Authors | Nayak, A.R. / Samso, M. | |||||||||||||||||||||
Funding support | United States, 6items
| |||||||||||||||||||||
Citation | Journal: Elife / Year: 2022 Title: Ca inactivation of the mammalian ryanodine receptor type 1 in a lipidic environment revealed by cryo-EM. Authors: Ashok R Nayak / Montserrat Samsó / Abstract: Activation of the intracellular Ca channel ryanodine receptor (RyR) triggers a cytosolic Ca surge, while elevated cytosolic Ca inhibits the channel in a negative feedback mechanism. Cryogenic ...Activation of the intracellular Ca channel ryanodine receptor (RyR) triggers a cytosolic Ca surge, while elevated cytosolic Ca inhibits the channel in a negative feedback mechanism. Cryogenic electron microscopy of rabbit RyR1 embedded in nanodiscs under partially inactivating Ca conditions revealed an open and a closed-inactivated conformation. Ca binding to the high-affinity site engages the central and C-terminal domains into a block, which pries the S6 four-helix bundle open. Further rotation of this block pushes S6 toward the central axis, closing (inactivating) the channel. Main characteristics of the Ca-inactivated conformation are downward conformation of the cytoplasmic assembly and tightly knit subunit interface contributed by a fully occupied Ca activation site, two inter-subunit resolved lipids, and two salt bridges between the EF hand domain and the S2-S3 loop validated by disease-causing mutations. The structural insight illustrates the prior Ca activation prerequisite for Ca inactivation and provides for a seamless transition from inactivated to closed conformations. | |||||||||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7k0t.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7k0t.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7k0t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7k0t_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7k0t_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7k0t_validation.xml.gz | 338.7 KB | Display | |
Data in CIF | 7k0t_validation.cif.gz | 561.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/7k0t ftp://data.pdbj.org/pub/pdb/validation_reports/k0/7k0t | HTTPS FTP |
-Related structure data
Related structure data | 22616MC 7tdgC 7tdhC 7tdiC 7tdjC 7tdkC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-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 / Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Rabbit RyR1 with AMP-PCP / Type: COMPLEX Details: Purified RyR1 was reconstituted with membrane scaffold protein MSP1E3D1, and POPC. Entity ID: #1 / Source: NATURAL | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
| |||||||||||||||||||||||||||||||||||
Specimen | Conc.: 4.35 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: UltrAuFoil R1.2/1.3 | |||||||||||||||||||||||||||||||||||
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 |
---|---|
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: 130000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 70.3 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1959 |
EM imaging optics | Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 60 |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 52856 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21551 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |