+Open data
-Basic information
Entry | Database: PDB / ID: 2b1o | ||||||
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Title | Solution Structure of Ca2+-bound DdCAD-1 | ||||||
Components | Calcium-dependent cell adhesion molecule-1 | ||||||
Keywords | CELL ADHESION / DdCAD-1 / Calcium / Cell adherison | ||||||
Function / homology | Function and homology information sorocarp morphogenesis / contractile vacuole / sorocarp development / response to curcumin / aggregation involved in sorocarp development / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / biological process involved in interaction with symbiont / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / endocytic vesicle / ruffle ...sorocarp morphogenesis / contractile vacuole / sorocarp development / response to curcumin / aggregation involved in sorocarp development / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / biological process involved in interaction with symbiont / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / endocytic vesicle / ruffle / phagocytic vesicle / lipid droplet / extracellular matrix / filopodium / cell-cell junction / lamellipodium / cell cortex / regulation of gene expression / defense response to Gram-negative bacterium / calmodulin binding / external side of plasma membrane / calcium ion binding / extracellular region / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Dictyostelium discoideum (eukaryote) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Lin, Z. / Sriskanthadevan, S. / Huang, H.B. / Siu, C.H. / Yang, D.W. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2006 Title: Solution structures of the adhesion molecule DdCAD-1 reveal new insights into Ca(2+)-dependent cell-cell adhesion Authors: Lin, Z. / Sriskanthadevan, S. / Huang, H.B. / Siu, C.H. / Yang, D.W. #1: Journal: J.Biomol.Nmr / Year: 2004 Title: (1)H, (13)C and (15)N resonance assignments of Ca(2+)-free DdCAD-1: a Ca(2+)-dependent cell-cell adhesion molecule Authors: Lin, Z. / Huang, H.B. / Siu, C.H. / Yang, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b1o.cif.gz | 601.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b1o.ent.gz | 497.9 KB | Display | PDB format |
PDBx/mmJSON format | 2b1o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2b1o_validation.pdf.gz | 349.4 KB | Display | wwPDB validaton report |
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Full document | 2b1o_full_validation.pdf.gz | 412.6 KB | Display | |
Data in XML | 2b1o_validation.xml.gz | 39.8 KB | Display | |
Data in CIF | 2b1o_validation.cif.gz | 54.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/2b1o ftp://data.pdbj.org/pub/pdb/validation_reports/b1/2b1o | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 23818.545 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: cadA / Plasmid: pET-M / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P54657 |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.5mM DdCAD-1 U-15N, 13C; 5mM CaCl2, 10mM PIPES buffer, 2mM DTT, 0.05mM SODIUM AZIDE, 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 5mM CaCl2, 0.05mM SODIUM / pH: 6.2 / Pressure: 1 atm / Temperature: 303 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 / Details: Energy minimization in Amber force field | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10 |