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Yorodumi- PDB-4odb: Crystal structure of the T1L reovirus attachment protein sigma1 i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4odb | ||||||
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Title | Crystal structure of the T1L reovirus attachment protein sigma1 in complex with Junctional Adhesion Molecule-A | ||||||
Components |
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Keywords | VIRAL PROTEIN / immunoglobulin fold / greek key motif / beta spiral / viral attachment protein / capsid protein / viral receptor / cell adhesion molecule | ||||||
Function / homology | Function and homology information positive regulation of establishment of endothelial barrier / memory T cell extravasation / Tight junction interactions / establishment of endothelial intestinal barrier / regulation of membrane permeability / protein localization to bicellular tight junction / viral outer capsid / actomyosin structure organization / positive regulation of platelet aggregation / tight junction ...positive regulation of establishment of endothelial barrier / memory T cell extravasation / Tight junction interactions / establishment of endothelial intestinal barrier / regulation of membrane permeability / protein localization to bicellular tight junction / viral outer capsid / actomyosin structure organization / positive regulation of platelet aggregation / tight junction / regulation of bicellular tight junction assembly / intestinal absorption / negative regulation of stress fiber assembly / regulation of cytoskeleton organization / positive regulation of Rho protein signal transduction / maintenance of blood-brain barrier / leukocyte cell-cell adhesion / bicellular tight junction / Integrin cell surface interactions / regulation of cytokine production / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / PDZ domain binding / protein localization to plasma membrane / regulation of actin cytoskeleton organization / Cell surface interactions at the vascular wall / cell-cell adhesion / cellular response to mechanical stimulus / viral capsid / cell-cell junction / integrin binding / virus receptor activity / cell junction / regulation of cell shape / cell adhesion / cadherin binding / inflammatory response / symbiont entry into host cell / virion attachment to host cell / protein homodimerization activity / protein-containing complex / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | Mammalian orthoreovirus 1 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Stettner, E. / Stehle, T. | ||||||
Citation | Journal: To be Published Title: The JAM-A binding site is conserved in reovirus sigma1: Structure of the T1L sigma1-JAM-A complex Authors: Stettner, E. / Reiss, K. / Dietrich, M. / Stehle, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4odb.cif.gz | 164 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4odb.ent.gz | 131.3 KB | Display | PDB format |
PDBx/mmJSON format | 4odb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/4odb ftp://data.pdbj.org/pub/pdb/validation_reports/od/4odb | HTTPS FTP |
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-Related structure data
Related structure data | 3eoyS 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: 18791.027 Da / Num. of mol.: 3 / Fragment: Type 1 Lang sigma 1 head domain, residues 308-47 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mammalian orthoreovirus 1 / Strain: Lang / Gene: S1 / Plasmid: pET15-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P04506 #2: Protein | Mass: 11518.841 Da / Num. of mol.: 3 / Fragment: Ig-like V-type 1 domain, residues 28-129 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F11R, JAM1, JCAM, UNQ264/PRO301 / Plasmid: pGEX-4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9Y624 |
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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: 3.77 Å3/Da / Density % sol: 67.34 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 0.1 M MES, 17.1% PEG 20000, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 28, 2009 |
Radiation | Monochromator: double-channel cut fixed-exit monochromator for X-rays in the range from 6 to 17.5 keV; vertical collimation and focussing is achieved by mirrors. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. all: 22879 / Num. obs: 22673 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 70.01 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 3.2→3.28 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1643 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3EOY (modified with chainsaw) Resolution: 3.2→40.98 Å / Cor.coef. Fo:Fc: 0.8614 / Cor.coef. Fo:Fc free: 0.8261 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 81.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.5616 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→40.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.28 Å / Total num. of bins used: 11
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