+Open data
-Basic information
Entry | Database: PDB / ID: 4etu | ||||||
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Title | Crystal structure of rabbit ryanodine receptor 1 mutant R2939S | ||||||
Components | Ryanodine receptor 1 | ||||||
Keywords | METAL TRANSPORT / Ryanodine Receptor Calcium Release Channel / Phosphorylation / Muscle / Skeletal | ||||||
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 | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | ||||||
Authors | Yuchi, Z. / Lau, K. / Van Petegem, F. | ||||||
Citation | Journal: Structure / Year: 2012 Title: Disease mutations in the ryanodine receptor central region: crystal structures of a phosphorylation hot spot domain. Authors: Yuchi, Z. / Lau, K. / Van Petegem, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4etu.cif.gz | 54.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4etu.ent.gz | 37.1 KB | Display | PDB format |
PDBx/mmJSON format | 4etu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4etu_validation.pdf.gz | 439.8 KB | Display | wwPDB validaton report |
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Full document | 4etu_full_validation.pdf.gz | 441.6 KB | Display | |
Data in XML | 4etu_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 4etu_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/4etu ftp://data.pdbj.org/pub/pdb/validation_reports/et/4etu | HTTPS FTP |
-Related structure data
Related structure data | 4ertSC 4ervC 4esuC 4ettC 4etvC S: Starting model for refinement 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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Unit cell |
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-Components
#1: Protein | Mass: 24591.633 Da / Num. of mol.: 1 / Mutation: R2939S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RYR1 / Plasmid: pET28HMT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLacI / References: UniProt: P11716 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.09 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 15% PEG3350, 25% Glycerol, 0.1M HEPES, pH 7.0, vapor diffusion, hanging drop, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 8, 2012 / Details: Double Crystal Monochromator, mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: VARIMAX VHF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.19→116.42 Å / Num. all: 11510 / Num. obs: 11073 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.062 / Χ2: 1.004 / Net I/σ(I): 12.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ERT Resolution: 2.19→116.42 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.901 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.3 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.7 Å2 / Biso mean: 39.9603 Å2 / Biso min: 21.25 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→116.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.194→2.251 Å / Total num. of bins used: 20
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