+Open data
-Basic information
Entry | Database: PDB / ID: 5yws | ||||||
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Title | Crystal structure of TREX1 in complex with a Y structured DNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / DEDDh / Exouclease / Protein-DNA complex / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information immune response in brain or nervous system / adenyl deoxyribonucleotide binding / CD86 biosynthetic process / immune complex formation / cellular response to type I interferon / organ or tissue specific immune response / atrial cardiac muscle tissue development / activation of immune response / DNA synthesis involved in UV-damage excision repair / T cell antigen processing and presentation ...immune response in brain or nervous system / adenyl deoxyribonucleotide binding / CD86 biosynthetic process / immune complex formation / cellular response to type I interferon / organ or tissue specific immune response / atrial cardiac muscle tissue development / activation of immune response / DNA synthesis involved in UV-damage excision repair / T cell antigen processing and presentation / MutSalpha complex binding / retrotransposition / oligosaccharyltransferase complex / regulation of lysosome organization / DNA modification / regulation of lipid biosynthetic process / WW domain binding / regulation of fatty acid metabolic process / heart process / regulation of protein complex stability / MutLalpha complex binding / cellular response to hydroxyurea / lymphoid progenitor cell differentiation / double-stranded DNA 3'-5' DNA exonuclease activity / regulation of type I interferon production / exodeoxyribonuclease III / macrophage activation involved in immune response / regulation of tumor necrosis factor production / regulation of cellular respiration / inflammatory response to antigenic stimulus / DNA catabolic process / regulation of immunoglobulin production / apoptotic cell clearance / regulation of T cell activation / regulation of glycolytic process / DNA binding, bending / DNA duplex unwinding / 3'-5'-DNA exonuclease activity / DNA metabolic process / negative regulation of type I interferon-mediated signaling pathway / : / negative regulation of cGAS/STING signaling pathway / type I interferon-mediated signaling pathway / regulation of innate immune response / blood vessel development / mitotic G1 DNA damage checkpoint signaling / nuclear replication fork / cellular response to interferon-beta / generation of precursor metabolites and energy / heart morphogenesis / response to UV / 3'-5' exonuclease activity / negative regulation of innate immune response / DNA damage checkpoint signaling / kidney development / determination of adult lifespan / protein-DNA complex / cellular response to reactive oxygen species / establishment of protein localization / cellular response to gamma radiation / cellular response to UV / regulation of inflammatory response / double-stranded DNA binding / regulation of gene expression / single-stranded DNA binding / cellular response to oxidative stress / DNA replication / defense response to virus / adaptive immune response / protein stabilization / inflammatory response / immune response / innate immune response / DNA damage response / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / DNA binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Hsiao, Y.Y. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: PLoS Biol. / Year: 2018 Title: Structural basis for overhang excision and terminal unwinding of DNA duplexes by TREX1 Authors: Huang, K.W. / Liu, T.C. / Liang, R.Y. / Chu, L.Y. / Cheng, H.L. / Chu, J.W. / Hsiao, Y.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yws.cif.gz | 336.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yws.ent.gz | 272.4 KB | Display | PDB format |
PDBx/mmJSON format | 5yws.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yws_validation.pdf.gz | 457.2 KB | Display | wwPDB validaton report |
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Full document | 5yws_full_validation.pdf.gz | 461.1 KB | Display | |
Data in XML | 5yws_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 5yws_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/5yws ftp://data.pdbj.org/pub/pdb/validation_reports/yw/5yws | HTTPS FTP |
-Related structure data
Related structure data | 5ywtC 5ywuC 5ywvC 3mxmS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 29876.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trex1 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RIPL / References: UniProt: Q91XB0, exodeoxyribonuclease III #2: DNA chain | Mass: 6710.313 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: Chemical | ChemComp-MG / #4: 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: 1.99 Å3/Da / Density % sol: 38.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1M SODIUM ACETATE TRIHYDRATE PH 4.5, 30%(V/V) POLYETHYLENE GLYCOL 300, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K PH range: 4.5 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 6, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.33 Å / Num. obs: 39153 / % possible obs: 97.4 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 31.4 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 3.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MXM Resolution: 2→29.33 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→29.33 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -21.7487 Å / Origin y: 15.3406 Å / Origin z: -11.9242 Å
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Refinement TLS group | Selection details: ALL |