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Yorodumi- PDB-2o39: Human Adenovirus type 11 knob in complex with domains SCR1 and SC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2o39 | |||||||||
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Title | Human Adenovirus type 11 knob in complex with domains SCR1 and SCR2 of CD46 (membrane cofactor protein, MCP) | |||||||||
Components |
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Keywords | VIRAL PROTEIN/immune system / Membrane cofactor protein / MCP / CD46 / Adenovirus / fiber knob / Ad11 / virus receptor complex / SCR / Short consensus repeat / CCP / complement control protein / VIRAL PROTEIN-immune system COMPLEX | |||||||||
Function / homology | Function and homology information sequestering of extracellular ligand from receptor / inner acrosomal membrane / regulation of Notch signaling pathway / negative regulation of complement activation, classical pathway / positive regulation of transforming growth factor beta production / T cell mediated immunity / positive regulation of memory T cell differentiation / positive regulation of regulatory T cell differentiation / adhesion receptor-mediated virion attachment to host cell / positive regulation of interleukin-10 production ...sequestering of extracellular ligand from receptor / inner acrosomal membrane / regulation of Notch signaling pathway / negative regulation of complement activation, classical pathway / positive regulation of transforming growth factor beta production / T cell mediated immunity / positive regulation of memory T cell differentiation / positive regulation of regulatory T cell differentiation / adhesion receptor-mediated virion attachment to host cell / positive regulation of interleukin-10 production / single fertilization / positive regulation of T cell proliferation / complement activation, classical pathway / Regulation of Complement cascade / viral capsid / virus receptor activity / signaling receptor activity / adaptive immune response / cell adhesion / cadherin binding / symbiont entry into host cell / negative regulation of gene expression / innate immune response / focal adhesion / host cell nucleus / positive regulation of gene expression / cell surface / extracellular space / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | Human adenovirus 11p Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | |||||||||
Authors | Persson, D.B. / Reiter, D.M. / Arnberg, N. / Stehle, T. | |||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2007 Title: Adenovirus type 11 binding alters the conformation of its receptor CD46. Authors: Persson, B.D. / Reiter, D.M. / Marttila, M. / Mei, Y.F. / Casasnovas, J.M. / Arnberg, N. / Stehle, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o39.cif.gz | 142.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o39.ent.gz | 112 KB | Display | PDB format |
PDBx/mmJSON format | 2o39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2o39_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2o39_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2o39_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 2o39_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/2o39 ftp://data.pdbj.org/pub/pdb/validation_reports/o3/2o39 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Trimer consisting of three Ad11 chains and three CD46 SCR1 and SCR2 chains. The asymmetric unit contains two copies of an Ad11 chain, belonging to different trimers, and two copies of CD46, also belonging to different trimers. The biological units, the trimers, can be created through application of crystallographic symmetry operators. |
-Components
#1: Protein | Mass: 22046.545 Da / Num. of mol.: 2 / Fragment: residues 129-325 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human adenovirus 11p / Genus: Mastadenovirus / Species: Human adenovirus B / Strain: Slobiski / Gene: PIV / Plasmid: Pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 DE3 / References: UniProt: P35774 #2: Protein | Mass: 14517.551 Da / Num. of mol.: 2 / Fragment: SCR1 and SCR 2 domains Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD46, MCP / Plasmid: pBJ5 / Cell (production host): CHO cell / Cell line (production host): CHO-LEC3281 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P15529 #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 35% PEG 200, 200mM CaCl2, 100mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 10, 2006 |
Radiation | Monochromator: Undulator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→40 Å / Num. all: 20127 / Num. obs: 18738 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 7.23 |
Reflection shell | Resolution: 2.85→2.95 Å / Redundancy: 4 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2.64 / Num. unique all: 1710 / % possible all: 83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Human Adenovirus type 11 (unpublished) CD46 SCR1 and SCR2 Resolution: 2.85→40 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.85→40 Å
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Refine LS restraints |
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