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- PDB-5ywt: Crystal structure of TREX1 in complex with a duplex DNA with 3' o... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ywt | ||||||
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Title | Crystal structure of TREX1 in complex with a duplex DNA with 3' overhang | ||||||
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![]() | DNA BINDING PROTEIN / TREX1 / exonuclease / DEDDh family / protein-DNA complex / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() 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 / regulation of fatty acid metabolic process / regulation of lipid biosynthetic process / DNA modification / WW domain binding / heart process / MutLalpha complex binding / regulation of protein complex stability / cellular response to hydroxyurea / lymphoid progenitor cell differentiation / regulation of type I interferon production / double-stranded DNA 3'-5' DNA exonuclease activity / 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 duplex unwinding / DNA binding, bending / 3'-5'-DNA exonuclease activity / negative regulation of type I interferon-mediated signaling pathway / DNA metabolic process / : / negative regulation of cGAS/STING signaling pathway / type I interferon-mediated signaling pathway / regulation of innate immune response / blood vessel development / nuclear replication fork / cellular response to interferon-beta / heart morphogenesis / response to UV / mitotic G1 DNA damage checkpoint signaling / negative regulation of innate immune response / 3'-5' exonuclease activity / DNA damage checkpoint signaling / generation of precursor metabolites and energy / kidney development / determination of adult lifespan / protein-DNA complex / establishment of protein localization / cellular response to gamma radiation / cellular response to reactive oxygen species / cellular response to UV / single-stranded DNA binding / cellular response to oxidative stress / regulation of inflammatory response / regulation of gene expression / double-stranded DNA binding / defense response to virus / adaptive immune response / DNA replication / 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 | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hsiao, Y.Y. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 301.3 KB | Display | ![]() |
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PDB format | ![]() | 243.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.5 KB | Display | ![]() |
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Full document | ![]() | 465.2 KB | Display | |
Data in XML | ![]() | 24.5 KB | Display | |
Data in CIF | ![]() | 36.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ywsC ![]() 5ywuC ![]() 5ywvC ![]() 3mxmS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() #2: DNA chain | Mass: 5763.708 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | ChemComp-MG / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.59 Å3/Da / Density % sol: 22.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M BICINE PH 8.5, 20%(W/V) POLYETHYLENE GLYCOL 10,000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jul 25, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 50099 / % possible obs: 98.2 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 2.3 / % possible all: 96.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3MXM Resolution: 1.7→28.79 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.34 / Phase error: 21.42
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→28.79 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: -7.3623 Å / Origin y: -7.6745 Å / Origin z: 19.979 Å
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Refinement TLS group | Selection details: ALL |