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- PDB-3b6p: Structure of TREX1 in complex with a nucleotide and inhibitor ion... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3b6p | ||||||
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Title | Structure of TREX1 in complex with a nucleotide and inhibitor ions (sodium and zinc) | ||||||
![]() | Three prime repair exonuclease 1 | ||||||
![]() | HYDROLASE / TREX1 / DEDD / exonuclease / DnaQ / sodium / zinc / catalysis / inhibition / deoxy-thimidine monophosphate (dTMP) / DNA damage / DNA repair / Magnesium / Nucleus / Phosphorylation | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Brucet, M. / Querol-Audi, J. / Fita, I. / Celada, A. | ||||||
![]() | ![]() Title: Structural and biochemical studies of TREX1 inhibition by metals. Identification of a new active histidine conserved in DEDDh exonucleases. Authors: Brucet, M. / Querol-Audi, J. / Bertlik, K. / Lloberas, J. / Fita, I. / Celada, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 188.6 KB | Display | ![]() |
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PDB format | ![]() | 148.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 37.8 KB | Display | |
Data in CIF | ![]() | 52.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3b6oC ![]() 2o4gS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 6 / Auth seq-ID: 9 - 234 / Label seq-ID: 11 - 236
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Components
#1: Protein | Mass: 27173.010 Da / Num. of mol.: 4 / Fragment: TREX1 exonuclease, UNP residues 9-245 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-TMP / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Crystallization: 22% PEG3350, 100 mM MES pH 6.0, 200 mM Li2SO4. Soaking: 24h, 22% PEG3350, 100 mM MES pH 6.0, 50 mM Li2SO4, 200 mM Na2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 20, 2006 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 48939 / Num. obs: 48939 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.118 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.486 / % possible all: 85.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ID 2o4g Resolution: 2.3→24.18 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.881 / SU B: 17.621 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.456 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.1 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→24.18 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 2868 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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