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Yorodumi- PDB-1t3l: Structural Analysis of the Voltage-Dependent Calcium Channel Beta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t3l | ||||||
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Title | Structural Analysis of the Voltage-Dependent Calcium Channel Beta Subunit Functional Core in Complex with Alpha1 Interaction Domain | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / protein-peptide complex / SH3 domain / Guanylate Kinase domain | ||||||
Function / homology | Function and homology information voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / voltage-gated calcium channel activity involved in AV node cell action potential / membrane depolarization during atrial cardiac muscle cell action potential / positive regulation of muscle contraction / high voltage-gated calcium channel activity / L-type voltage-gated calcium channel complex / photoreceptor ribbon synapse / positive regulation of calcium ion transport / calcium ion import / cellular response to caffeine ...voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / voltage-gated calcium channel activity involved in AV node cell action potential / membrane depolarization during atrial cardiac muscle cell action potential / positive regulation of muscle contraction / high voltage-gated calcium channel activity / L-type voltage-gated calcium channel complex / photoreceptor ribbon synapse / positive regulation of calcium ion transport / calcium ion import / cellular response to caffeine / calcium ion import across plasma membrane / regulation of heart rate by cardiac conduction / regulation of ryanodine-sensitive calcium-release channel activity / voltage-gated calcium channel activity / muscle contraction / release of sequestered calcium ion into cytosol / T-tubule / visual perception / calcium ion transmembrane transport / actin filament binding / presynapse / chemical synaptic transmission / transmembrane transporter binding / calmodulin binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Opatowsky, Y. / Chen, C.-C. / Campbell, K.P. / Hirsch, J.A. | ||||||
Citation | Journal: NEURON / Year: 2004 Title: Structural Analysis of Voltage-Dependent Calcium Channel Beta Subunit Functional Core and Its Complex with the Alpha1 Interaction Domain Authors: Opatowsky, Y. / Chen, C.-C. / Campbell, K.P. / Hirsch, J.A. #1: Journal: To be published Title: Expression, Purification and Crystallization of a Functional Core of the Voltage-Dependent Calcium Channel Beta Subunit Authors: Opatowsky, Y. / Chomsky-Hecht, O. / Hirsch, J.A. | ||||||
History |
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Remark 999 | SEQUENCE THE SEQUENCE OF THE PROTEIN IS FROM SWISSPROT P54288, ISOFORM 2A. RESIDUES 138-141 IN THE ...SEQUENCE THE SEQUENCE OF THE PROTEIN IS FROM SWISSPROT P54288, ISOFORM 2A. RESIDUES 138-141 IN THE COORDINATES WERE INTRODUCED INTO THE PROTEIN. THEY REPLACE RESIDUES 138-202 FROM THE NATIVE SEQUENCE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t3l.cif.gz | 79.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t3l.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 1t3l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t3l_validation.pdf.gz | 376 KB | Display | wwPDB validaton report |
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Full document | 1t3l_full_validation.pdf.gz | 382.3 KB | Display | |
Data in XML | 1t3l_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 1t3l_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/1t3l ftp://data.pdbj.org/pub/pdb/validation_reports/t3/1t3l | HTTPS FTP |
-Related 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: 38340.953 Da / Num. of mol.: 1 / Fragment: Functional Core (Residues 25-422) / Mutation: P122R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CACNB2, CACNLB2 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P54288 |
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#2: Protein/peptide | Mass: 2184.363 Da / Num. of mol.: 1 / Fragment: AID / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is from Oryctolagus cuniculus (rabbit) gene CACNA1S. References: UniProt: P07293 |
#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: 2.58 Å3/Da / Density % sol: 52.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: PEG 20K, Bicine, sodium chloride, beta-mercaptoethanol, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0069 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 7, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0069 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 19123 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.059 / Net I/σ(I): 21.3 |
Reflection shell | Highest resolution: 2.2 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.9 / % possible all: 63.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→84.52 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.895 / SU B: 7.447 / SU ML: 0.186 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.264 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.992 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→84.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20 /
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