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Open data
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Basic information
Entry | Database: PDB / ID: 7tqn | ||||||
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Title | Structure of human TREX1 | ||||||
![]() | Three-prime repair exonuclease 1 | ||||||
![]() | HYDROLASE / nuclease / DNase / innate immunity / autoimmunity | ||||||
Function / homology | ![]() 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 / 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 / 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 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 / blood vessel development / nuclear replication fork / cellular response to interferon-beta / mismatch repair / heart morphogenesis / mitotic G1 DNA damage checkpoint signaling / negative regulation of innate immune response / 3'-5' exonuclease activity / 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 / nuclear envelope / single-stranded DNA binding / regulation of inflammatory response / double-stranded DNA binding / DNA recombination / defense response to virus / DNA replication / protein stabilization / DNA repair / endoplasmic reticulum membrane / magnesium ion binding / protein homodimerization activity / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhou, W. / Richmond-Buccola, D. / Kranzusch, P.J. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.1 KB | Display | ![]() |
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PDB format | ![]() | 75 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 408.7 KB | Display | ![]() |
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Full document | ![]() | 409.4 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 14.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7tqoC ![]() 7tqpC ![]() 7tqqC ![]() 3mxjS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26180.080 Da / Num. of mol.: 1 / Mutation: A5T/P8H/P10H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.78 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M Sodium chloride, 0.1 M Bis-Tris pH 5.5, 20% PEG-3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 4, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→41.86 Å / Num. obs: 19529 / % possible obs: 99.5 % / Redundancy: 13.1 % / Biso Wilson estimate: 28.22 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.044 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.8→1.84 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1133 / CC1/2: 0.488 / Rpim(I) all: 0.798 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3MXJ Resolution: 1.8→41.86 Å / SU ML: 0.1977 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.6166 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: 33.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→41.86 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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