+Open data
-Basic information
Entry | Database: PDB / ID: 8hcc | ||||||
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Title | Crystal structure of mTREX1-RNA product complex (AMP) | ||||||
Components | Three-prime repair exonuclease 1 | ||||||
Keywords | HYDROLASE / TREX1 / DEDDh exonuclease / DNase / RNase / AMP | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Hsiao, Y.Y. / Huang, K.W. / Wu, C.Y. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2023 Title: Molecular insight into the specific enzymatic properties of TREX1 revealing the diverse functions in processing RNA and DNA/RNA hybrids. Authors: Huang, K.W. / Wu, C.Y. / Toh, S.I. / Liu, T.C. / Tu, C.I. / Lin, Y.H. / Cheng, A.J. / Kao, Y.T. / 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 | 8hcc.cif.gz | 544.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hcc.ent.gz | 449.4 KB | Display | PDB format |
PDBx/mmJSON format | 8hcc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/8hcc ftp://data.pdbj.org/pub/pdb/validation_reports/hc/8hcc | HTTPS FTP |
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-Related structure data
Related structure data | 8hcdC 8hceC 8hcfC 8hcgC 8hchC 5ywsS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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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.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trex1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q91XB0, exodeoxyribonuclease III #2: Chemical | ChemComp-AMP / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-NA / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 1.92 Å3/Da / Density % sol: 35.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M Magnesium acetate tetrahydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 20% w/v Polyethylene glycol 8,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Sep 22, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→30 Å / Num. obs: 61417 / % possible obs: 99.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.042 / Rrim(I) all: 0.085 / Χ2: 1.71 / Net I/σ(I): 12.2 / Num. measured all: 252782 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YWS Resolution: 2→27.164 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 137.18 Å2 / Biso mean: 36.1577 Å2 / Biso min: 15.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→27.164 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 12.3214 Å / Origin y: 1.0209 Å / Origin z: 29.5066 Å
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Refinement TLS group |
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