+Open data
-Basic information
Entry | Database: PDB / ID: 1yhp | ||||||
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Title | Solution Structure of Ca2+-free DdCAD-1 | ||||||
Components | Calcium-dependent cell adhesion molecule-1 | ||||||
Keywords | CELL ADHESION / DdCAD-1 / Calcium | ||||||
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 / phagocytic vesicle ...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 / phagocytic vesicle / ruffle / extracellular matrix / lipid droplet / 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. / 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 | 1yhp.cif.gz | 598.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yhp.ent.gz | 498.3 KB | Display | PDB format |
PDBx/mmJSON format | 1yhp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yhp_validation.pdf.gz | 351.2 KB | Display | wwPDB validaton report |
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Full document | 1yhp_full_validation.pdf.gz | 409.3 KB | Display | |
Data in XML | 1yhp_validation.xml.gz | 38.8 KB | Display | |
Data in CIF | 1yhp_validation.cif.gz | 53 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/1yhp ftp://data.pdbj.org/pub/pdb/validation_reports/yh/1yhp | HTTPS FTP |
-Related structure data
Related structure data | 2b1oC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-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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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample conditions | Ionic strength: 10mM PIPES, 0.05mM sodium azide / pH: 6.2 / Pressure: 1 atm / Temperature: 303 K |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 Details: the structures are based on a total of 4847 restraints, 4481 are NOE-derived distance constraints, 212 dihedral angle restraints,154 distance restraints from hydrogen bonds | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 |