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Yorodumi- PDB-6sit: Pseudo-atomic crystal structure of the desmoglein 2 - human adeno... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sit | |||||||||
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Title | Pseudo-atomic crystal structure of the desmoglein 2 - human adenovirus serotype 3 fibre knob complex | |||||||||
Components |
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Keywords | VIRAL PROTEIN / virus receptor / extracellular domain / cell surface glycoprotein / desmosome | |||||||||
Function / homology | Function and homology information Purkinje myocyte development / bundle of His cell-Purkinje myocyte adhesion involved in cell communication / cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication / desmosome organization / Keratinization / desmosome / Formation of the cornified envelope / cornified envelope / regulation of ventricular cardiac muscle cell action potential / Apoptotic cleavage of cell adhesion proteins ...Purkinje myocyte development / bundle of His cell-Purkinje myocyte adhesion involved in cell communication / cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication / desmosome organization / Keratinization / desmosome / Formation of the cornified envelope / cornified envelope / regulation of ventricular cardiac muscle cell action potential / Apoptotic cleavage of cell adhesion proteins / adhesion receptor-mediated virion attachment to host cell / homophilic cell adhesion via plasma membrane adhesion molecules / regulation of heart rate by cardiac conduction / intercalated disc / RHOG GTPase cycle / lateral plasma membrane / RAC2 GTPase cycle / RAC3 GTPase cycle / maternal process involved in female pregnancy / cell adhesion molecule binding / response to progesterone / cell-cell adhesion / viral capsid / cell-cell junction / cell junction / cell adhesion / symbiont entry into host cell / apical plasma membrane / intracellular membrane-bounded organelle / calcium ion binding / host cell nucleus / cell surface / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | Human adenovirus B3 Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å | |||||||||
Authors | Burmeister, W.P. / Fender, P. / Vassal-Stermann, E. | |||||||||
Funding support | France, 2items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2019 Title: Intermediate-resolution crystal structure of the human adenovirus B serotype 3 fibre knob in complex with the EC2-EC3 fragment of desmoglein 2. Authors: Vassal-Stermann, E. / Hutin, S. / Fender, P. / Burmeister, W.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sit.cif.gz | 101 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sit.ent.gz | 75 KB | Display | PDB format |
PDBx/mmJSON format | 6sit.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/si/6sit ftp://data.pdbj.org/pub/pdb/validation_reports/si/6sit | HTTPS FTP |
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-Related structure data
Related structure data | 1h7zS 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
#1: Protein | Mass: 21270.014 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human adenovirus B3 / Gene: L5 / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: P04501 | ||
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#2: Protein | Mass: 26609.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: extracellular domain EC2 and EC3 / Source: (gene. exp.) Homo sapiens (human) / Gene: DSG2, CDHF5 / Plasmid: pETM-40 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: Q14126 | ||
#3: Chemical | ChemComp-CA / Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.07 % / Description: prisms |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 7 mg/mL complex in 20 mM Tris-HCl, pH 8, 150 mM NaCl, 3 mM CaCl2 using a reservoir solution of 15 % PEG 3350, 0.2 M (NH4)2SO4, 0.1 M Na-acetate pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å | |||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Apr 12, 2018 Details: Vertically focused by CRLs and horizontally focussed by a mirror in half-Kirkpatrick-Baez (KB) geometry | |||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||
Reflection | Resolution: 4.49→46.51 Å / Num. obs: 3184 / % possible obs: 97.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 233 Å2 / CC1/2: 0.997 / R split: 0.093 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.053 / Rrim(I) all: 0.108 / Χ2: 0.77 / Net I/av σ(I): 4.9 / Net I/σ(I): 6.5 | |||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1h7z Resolution: 4.5→46.5 Å / SU R Cruickshank DPI: 1.7 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 252.167 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 382.5 Å2 / Biso mean: 252 Å2 / Biso min: 256.54 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 4.5→46.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.5→4.7 Å
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Xplor file |
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