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- PDB-4i8m: Crystal structure of rabbit Ryanodine receptor 1 (residues 1-536)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4i8m | ||||||
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Title | Crystal structure of rabbit Ryanodine receptor 1 (residues 1-536) disease mutant V219I | ||||||
![]() | Ryanodine receptor 1 | ||||||
![]() | METAL TRANSPORT / CALCIUM CHANNEL / SR/ER MEMBRANE | ||||||
Function / homology | ![]() 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 ...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 / toxic substance binding / smooth endoplasmic reticulum / voltage-gated calcium channel activity / skeletal muscle fiber development / striated muscle contraction / muscle contraction / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / cellular response to calcium ion / sarcoplasmic reticulum / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kimlicka, L. / Van Petegem, F. | ||||||
![]() | ![]() Title: Disease mutations in the ryanodine receptor N-terminal region couple to a mobile intersubunit interface. Authors: Kimlicka, L. / Lau, K. / Tung, C.C. / Van Petegem, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 195.6 KB | Display | ![]() |
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PDB format | ![]() | 158.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4i0yC ![]() 4i1eC ![]() 4i2sC ![]() 4i37C ![]() 4i3nC ![]() 4i6iC ![]() 4i7iC ![]() 4i96C ![]() 2xoaS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 59490.406 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DISEASE HOT SPOT, RESIDUES 1-536 / Mutation: V219I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 7.08 Å3/Da / Density % sol: 82.63 % |
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Crystal grow | Method: evaporation / pH: 9 / Details: pH 9.0, EVAPORATION |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
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Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 9, 2010 | |||||||||||||||||||||
Radiation | Monochromator: ACCEL/BRUKER DOUBLE CRYSTAL MONOCHROMATOR (DCM) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.8→48.86 Å / Num. obs: 41721 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.1 % | |||||||||||||||||||||
Reflection shell |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 2XOA Resolution: 2.8→46.94 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.918 / SU B: 22.39 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.643 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→46.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.872 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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