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Yorodumi- PDB-5erp: Crystal structure of human Desmocollin-2 ectodomain fragment EC2-5 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5erp | |||||||||
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Title | Crystal structure of human Desmocollin-2 ectodomain fragment EC2-5 | |||||||||
Components | Desmocollin-2 | |||||||||
Keywords | CELL ADHESION / extracellular cadherin domain / cell surface / desmosome | |||||||||
Function / homology | Function and homology information cardiac muscle cell-cardiac muscle cell adhesion / bundle of His cell-Purkinje myocyte adhesion involved in cell communication / cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication / Keratinization / desmosome / Formation of the cornified envelope / cornified envelope / regulation of ventricular cardiac muscle cell action potential / homophilic cell adhesion via plasma membrane adhesion molecules / regulation of heart rate by cardiac conduction ...cardiac muscle cell-cardiac muscle cell adhesion / bundle of His cell-Purkinje myocyte adhesion involved in cell communication / cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication / Keratinization / desmosome / Formation of the cornified envelope / cornified envelope / regulation of ventricular cardiac muscle cell action potential / homophilic cell adhesion via plasma membrane adhesion molecules / regulation of heart rate by cardiac conduction / intercalated disc / cellular response to starvation / adherens junction / cell-cell adhesion / cytoplasmic vesicle / cell adhesion / calcium ion binding / endoplasmic reticulum / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Harrison, O.J. / Brasch, J. / Shapiro, L. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Structural basis of adhesive binding by desmocollins and desmogleins. Authors: Harrison, O.J. / Brasch, J. / Lasso, G. / Katsamba, P.S. / Ahlsen, G. / Honig, B. / Shapiro, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5erp.cif.gz | 354.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5erp.ent.gz | 291.4 KB | Display | PDB format |
PDBx/mmJSON format | 5erp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5erp_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5erp_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5erp_validation.xml.gz | 35.9 KB | Display | |
Data in CIF | 5erp_validation.cif.gz | 48.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/5erp ftp://data.pdbj.org/pub/pdb/validation_reports/er/5erp | HTTPS FTP |
-Related structure data
Related structure data | 5eqxC 5erdSC 5iryC 5j5jC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 50331.996 Da / Num. of mol.: 2 / Fragment: unp residues 236-680 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DSC2, CDHF2, DSC3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q02487 |
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-Sugars , 3 types, 14 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-MAN / #4: Sugar | |
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-Non-polymers , 4 types, 139 molecules
#5: Chemical | ChemComp-CA / #6: Chemical | #7: Chemical | ChemComp-EDO / #8: Water | ChemComp-HOH / | |
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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: 4.43 Å3/Da / Density % sol: 72.24 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% (w/v) EDO_P8K (Molecular Dimensions), 10% amino acids mix (Molecular Dimensions), 0.1M MES-imidazole pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 45932 / % possible obs: 98 % / Redundancy: 3.8 % / Net I/σ(I): 12.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ERD Resolution: 2.7→79.121 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→79.121 Å
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Refine LS restraints |
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LS refinement shell |
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