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Yorodumi- PDB-7f05: Crystal structure of human cardiac calsequestrin bound with calcium -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f05 | ||||||
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Title | Crystal structure of human cardiac calsequestrin bound with calcium | ||||||
Components | Calsequestrin-2 | ||||||
Keywords | METAL BINDING PROTEIN / calcium binding / cardiac SR / polymer | ||||||
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 / SAD / Resolution: 2.298 Å | ||||||
Authors | Fan, X.X. / Liu, X.X. / Su, X.D. / Wang, S.Q. | ||||||
Citation | Journal: To Be Published Title: Ca2+-dependent Formation of a Non-transmembrane Channel in a Calsequestrin-2 Dimer Authors: Fan, X.X. / Liu, Z.H. / Yu, H. / Liu, X.Y. / Li, L.L. / Wang, L.P. / Li, H.T. / Huang, X.Y. / Xu, Z. / Su, X.D. / Song, C. / Guo, X.F. / Wang, S.Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f05.cif.gz | 335.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f05.ent.gz | 263.9 KB | Display | PDB format |
PDBx/mmJSON format | 7f05.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/7f05 ftp://data.pdbj.org/pub/pdb/validation_reports/f0/7f05 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 46800.602 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASQ2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O14958 #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.78 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM Na cacodylate (pH 6.0), 25% (vol/vol) 2-methyl-2,4-pentanedio (MPD), and 40 mM calcium lactate. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 8, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.298→78.569 Å / Num. obs: 74946 / % possible obs: 99.5 % / Redundancy: 10.7 % / Biso Wilson estimate: 26.99 Å2 / Rpim(I) all: 0.046 / Rrim(I) all: 0.151 / Rsym value: 0.144 / Net I/av σ(I): 4.4 / Net I/σ(I): 14.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.298→19.744 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.46 / Stereochemistry target values: MLHL
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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: 158.18 Å2 / Biso mean: 36.06 Å2 / Biso min: 9.87 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.298→19.744 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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