+Open data
-Basic information
Entry | Database: PDB / ID: 7tqp | ||||||
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Title | Structure of human TREX1 | ||||||
Components | Three-prime repair exonuclease 1 | ||||||
Keywords | HYDROLASE / nuclease / DNase / innate immunity / autoimmunity | ||||||
Function / homology | Function and homology information Regulation by TREX1 / immune response in brain or nervous system / adenyl deoxyribonucleotide binding / CD86 biosynthetic process / immune complex formation / 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 ...Regulation by TREX1 / immune response in brain or nervous system / adenyl deoxyribonucleotide binding / CD86 biosynthetic process / immune complex formation / 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 / IRF3-mediated induction of type I IFN / 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 / blood vessel development / mitotic G1 DNA damage checkpoint signaling / nuclear replication fork / cellular response to interferon-beta / generation of precursor metabolites and energy / mismatch repair / heart morphogenesis / 3'-5' exonuclease activity / negative regulation of innate immune response / kidney development / determination of adult lifespan / protein-DNA complex / cellular response to reactive oxygen species / establishment of protein localization / cellular response to gamma radiation / nuclear envelope / regulation of inflammatory response / double-stranded DNA binding / single-stranded DNA binding / DNA replication / DNA recombination / defense response to virus / protein stabilization / DNA repair / endoplasmic reticulum membrane / magnesium ion binding / protein homodimerization activity / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Zhou, W. / Richmond-Buccola, D. / Kranzusch, P.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis of human TREX1 DNA degradation and autoimmune disease. Authors: Zhou, W. / Richmond-Buccola, D. / Wang, Q. / Kranzusch, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tqp.cif.gz | 121 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tqp.ent.gz | 76.3 KB | Display | PDB format |
PDBx/mmJSON format | 7tqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tqp_validation.pdf.gz | 442.9 KB | Display | wwPDB validaton report |
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Full document | 7tqp_full_validation.pdf.gz | 443.7 KB | Display | |
Data in XML | 7tqp_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 7tqp_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/7tqp ftp://data.pdbj.org/pub/pdb/validation_reports/tq/7tqp | HTTPS FTP |
-Related structure data
Related structure data | 7tqnC 7tqoC 7tqqC 3mxjS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26281.133 Da / Num. of mol.: 1 Mutation: A5T, P8H, P10H, F17L, M19L, F26S, Q28R, K30E, C42R, S46N, P47T, P48S, T49I, P53H, T56P, P59R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TREX1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NSU2, exodeoxyribonuclease III | ||||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.98 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M NaCl, 0.1 M CHES pH 9.5, 1.26 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→42.47 Å / Num. obs: 16216 / % possible obs: 99.9 % / Redundancy: 21.6 % / Biso Wilson estimate: 32.92 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.049 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.95→2 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1098 / CC1/2: 0.403 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MXJ Resolution: 1.95→42.47 Å / SU ML: 0.2517 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.8267 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 36.04 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→42.47 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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