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Yorodumi- PDB-9e1d: Structure of RyR1 in the primed state in the presence of enprofylline -
+Open data
-Basic information
Entry | Database: PDB / ID: 9e1d | ||||||
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Title | Structure of RyR1 in the primed state in the presence of enprofylline | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / calcium channel / sarcoplasmic reticulum | ||||||
Function / homology | Function and homology information cytoplasmic side of membrane / 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 / organelle membrane / cellular response to caffeine ...cytoplasmic side of membrane / 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 / organelle membrane / cellular response to caffeine / outflow tract morphogenesis / intracellularly gated calcium channel activity / regulation of ryanodine-sensitive calcium-release channel activity / toxic substance binding / voltage-gated calcium channel activity / smooth endoplasmic reticulum / skeletal muscle fiber development / striated muscle contraction / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / release of sequestered calcium ion into cytosol / muscle contraction / sarcoplasmic reticulum membrane / cellular response to calcium ion / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / 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 / intracellular membrane-bounded organelle / calcium ion binding / ATP binding / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.76 Å | ||||||
Authors | Miotto, M.C. / Marks, A.R. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Targeting Ryanodine Receptors with Allopurinol and Xanthine Derivatives for the Treatment of Cardiac and Musculoskeletal Weakness Disorders Authors: Miotto, M.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9e1d.cif.gz | 3.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb9e1d.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9e1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9e1d_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 9e1d_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 9e1d_validation.xml.gz | 458.9 KB | Display | |
Data in CIF | 9e1d_validation.cif.gz | 690.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/9e1d ftp://data.pdbj.org/pub/pdb/validation_reports/e1/9e1d | HTTPS FTP |
-Related structure data
Related structure data | 47390MC 9e17C 9e18C 9e19C 9e1aC 9e1bC 9e1cC 9e1eC 9e1fC 9e1gC 9e1hC 9e1iC 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
-Protein , 2 types, 8 molecules ABDCEHGF
#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: Protein | Mass: 11967.705 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P62943, peptidylprolyl isomerase |
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-Non-polymers , 4 types, 16 molecules
#3: Chemical | ChemComp-ATP / #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-ZN / #6: Chemical | ChemComp-A1BD3 / Mass: 194.191 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10N4O2 / Feature type: SUBJECT OF INVESTIGATION |
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-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-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 |
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Source (natural) |
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Buffer solution | pH: 7.4 Details: 2 mM enprofylline was added to the final sample from a 100 mM stock solution in 100% DMSO. | |||||||||||||||||||||||||||||||||||||||||||||
Buffer component |
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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 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 80 K |
Image recording | Electron dose: 58 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Sampling size: 5 µm / Width: 5760 / Height: 4092 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94090 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7TZC Accession code: 7TZC / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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