- PDB-7u8y: TREX1 Structural Studies Capture Small Molecule Inhibition and Im... -
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Basic information
Entry
Database: PDB / ID: 7u8y
Title
TREX1 Structural Studies Capture Small Molecule Inhibition and Implicate Novel DNA Dynamics
Components
Three-prime repair exonuclease 1
Keywords
HYDROLASE/INHIBITOR / Inhibitor / Exonuclease / Immunotherapy / Complex / DNA BINDING PROTEIN / HYDROLASE-INHIBITOR complex
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 / 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
Evidence: gel filtration, TREX1 from gel filtration consistent with size of dimer. Also, there are many additional X-ray structures of TREX enzymes, all with the same dimer configuration.
Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interest
Y
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, sitting drop Details: Protein was dialyzed into 20 mM MES (pH 6.5) with 50 mM NaCl. Complex was formed by incubating the protein at 5 mg/mL with 2 mM dAMP and 5 mM MnCl2. 0.3 uL protein complex at 5 mg/ml TREX1 ...Details: Protein was dialyzed into 20 mM MES (pH 6.5) with 50 mM NaCl. Complex was formed by incubating the protein at 5 mg/mL with 2 mM dAMP and 5 mM MnCl2. 0.3 uL protein complex at 5 mg/ml TREX1 was mixed with an equal volume of reservoir solution and placed on a bridge above 50 uL of the reservoir solution. mTREX1-dAMP crystals grew in initial conditions of 0.2 M MES monohydrate, sodium hydroxide (pH 6.2), and 20% w/v polyethylene glycol 4,000. All crystals grew within one week. After crystal formation, 4 mM TIM009 was soaked into mTREX1-dAMP crystals for 5 days. Prior to data collection crystals were dipped into reservoir solution containing 15% glycerol in preparation for cryo-cooling
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Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Resolution: 2.22→45.5 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.347 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22175
1194
5.1 %
RANDOM
Rwork
0.18097
-
-
-
obs
0.18309
22068
97.29 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parameters
Biso mean: 49.402 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.08 Å2
-0.04 Å2
0 Å2
2-
-
-0.08 Å2
0 Å2
3-
-
-
0.26 Å2
Refinement step
Cycle: LAST / Resolution: 2.22→45.5 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3448
0
92
124
3664
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.017
3629
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.019
3390
X-RAY DIFFRACTION
r_angle_refined_deg
1.343
1.913
4968
X-RAY DIFFRACTION
r_angle_other_deg
1.074
2.637
7826
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.297
5
441
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
29.667
21.149
174
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.493
15
577
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.118
15
28
X-RAY DIFFRACTION
r_chiral_restr
0.085
0.2
549
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
4027
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
789
X-RAY DIFFRACTION
r_mcbond_it
2.077
2.593
1776
X-RAY DIFFRACTION
r_mcbond_other
2.044
2.59
1774
X-RAY DIFFRACTION
r_mcangle_it
2.954
3.876
2213
X-RAY DIFFRACTION
r_mcangle_other
2.926
3.875
2213
X-RAY DIFFRACTION
r_scbond_it
3.066
3.14
1853
X-RAY DIFFRACTION
r_scbond_other
3.065
3.141
1854
X-RAY DIFFRACTION
r_scangle_other
4.56
4.622
2751
X-RAY DIFFRACTION
r_long_range_B_refined
9.521
34.925
4407
X-RAY DIFFRACTION
r_long_range_B_other
9.529
34.819
4389
LS refinement shell
Resolution: 2.222→2.28 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.266
66
-
Rwork
0.208
1616
-
obs
-
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93.86 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
3.2641
0.2997
0.3164
2.2336
0.3604
3.2654
-0.1515
0.5598
0.1578
-0.3215
0.0042
0.048
-0.4229
-0.3891
0.1473
0.118
0.0196
-0.0565
0.1726
0.0102
0.0563
-27.02
-8.123
-6.008
2
2.5791
-0.1309
1.2013
2.3174
0.2623
3.1507
0.1045
-0.3995
-0.2337
0.3137
-0.0238
0.0362
0.3381
-0.3599
-0.0807
0.1101
-0.0459
-0.0305
0.0801
0.0357
0.0431
-19.558
-20.058
16.608
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
6 - 234
2
X-RAY DIFFRACTION
2
B
6 - 234
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