+Open data
-Basic information
Entry | Database: PDB / ID: 6owv | |||||||||||||||
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Title | Crystal structure of a Human Cardiac Calsequestrin Filament | |||||||||||||||
Components | Calsequestrin-2 | |||||||||||||||
Keywords | METAL BINDING PROTEIN / Calsequestrin / Calcium-Binding Proteins / Sarcoplasmic Reticulum Proteins | |||||||||||||||
Function / homology | Function and homology information calcium ion sequestering activity / negative regulation of potassium ion transmembrane transporter activity / regulation of cell communication by electrical coupling / junctional sarcoplasmic reticulum membrane / sequestering of calcium ion / Purkinje myocyte to ventricular cardiac muscle cell signaling / sarcoplasmic reticulum lumen / regulation of membrane repolarization / ion binding / cellular response to caffeine ...calcium ion sequestering activity / negative regulation of potassium ion transmembrane transporter activity / regulation of cell communication by electrical coupling / junctional sarcoplasmic reticulum membrane / sequestering of calcium ion / Purkinje myocyte to ventricular cardiac muscle cell signaling / sarcoplasmic reticulum lumen / regulation of membrane repolarization / ion binding / cellular response to caffeine / negative regulation of potassium ion transport / protein polymerization / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / striated muscle contraction / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cardiac muscle contraction / Ion homeostasis / sarcoplasmic reticulum membrane / calcium channel complex / regulation of heart rate / sarcoplasmic reticulum / Stimuli-sensing channels / Z disc / intracellular calcium ion homeostasis / calcium-dependent protein binding / calcium ion binding / protein homodimerization activity / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | |||||||||||||||
Authors | Titus, E.W. / Deiter, F.H. / Shi, C. / Jura, N. / Deo, R.C. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2020 Title: The structure of a calsequestrin filament reveals mechanisms of familial arrhythmia. Authors: Titus, E.W. / Deiter, F.H. / Shi, C. / Wojciak, J. / Scheinman, M. / Jura, N. / Deo, R.C. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6owv.cif.gz | 160.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6owv.ent.gz | 123.1 KB | Display | PDB format |
PDBx/mmJSON format | 6owv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/6owv ftp://data.pdbj.org/pub/pdb/validation_reports/ow/6owv | HTTPS FTP |
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-Related structure data
Related structure data | 6owwC 1sjiS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.2941360 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 44968.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASQ2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: O14958 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.89 % / Description: Rod |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, lithium sulfate / Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Cryo / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 22, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1158 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.88→71.06 Å / Num. obs: 35602 / % possible obs: 100 % / Redundancy: 22.5 % / Biso Wilson estimate: 47.702 Å2 / Rpim(I) all: 0.018 / Rrim(I) all: 0.086 / Net I/σ(I): 14.8 / Num. measured all: 799805 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SJI Resolution: 1.88→53.937 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 222.99 Å2 / Biso mean: 82.651 Å2 / Biso min: 38.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.88→53.937 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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