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Yorodumi- PDB-7umz: Cryo-EM structure of rabbit RyR1 in the presence of high Mg2+ and... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7umz | |||||||||||||||||||||
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Title | Cryo-EM structure of rabbit RyR1 in the presence of high Mg2+ and AMP-PCP in nanodisc | |||||||||||||||||||||
Components | Ryanodine receptor 1 | |||||||||||||||||||||
Keywords | TRANSPORT PROTEIN / Ryanodine Receptor / RyR1 / Intracellular Calcium channel / Mg2+ / Inhibition / Excitation-Contraction coupling | |||||||||||||||||||||
Function / homology | PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine Function and homology information | |||||||||||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.09 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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7umz.cif.gz | 2.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7umz.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7umz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/7umz ftp://data.pdbj.org/pub/pdb/validation_reports/um/7umz | HTTPS FTP |
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-Related structure data
Related structure data | 26610MC 7k0sC C: citing same article (ref.) M: map data used to model this data |
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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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 542887.000 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
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-Non-polymers , 5 types, 37 molecules
#2: Chemical | ChemComp-ACP / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-LBN / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Sequence details | Residues that could not be identified were recorded as UNK. The actual amino acid sequence is ...Residues that could not be identified were recorded as UNK. The actual amino acid sequence is identical to Uniprot P11716. |
-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 AMP-PCP and inhibiting Mg2+ / 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 Zeland White / Cellular location: Sarcoplasmic reticulum membrane / Organ: Skeletal Muscle / Organelle: Sarcoplasmic reticulum |
Buffer solution | pH: 7.4 Details: 20 mM MOPS (pH=7.4), 635mM KCl, 2mM DTT, 11.6mM MgCl2, 1mM AMP-PCP |
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 at a 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: 100 % / Chamber temperature: 277 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 FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 2000 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 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 9140 |
EM imaging optics | Energyfilter slit width: 10 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 525190 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 167778 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |