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- PDB-9kjl: The mTREX1-NSC 37204 complex structure by soaking in Soaking Cond... -

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Basic information

Entry
Database: PDB / ID: 9kjl
TitleThe mTREX1-NSC 37204 complex structure by soaking in Soaking Condition 3 (NSC 37204 complex 2)
ComponentsThree-prime repair exonuclease 1
KeywordsHYDROLASE / TREX1 / Inhibitor / DEDDh exonuclease
Function / homology
Function and homology information


immune response in brain or nervous system / immune complex formation / T cell antigen processing and presentation / organ or tissue specific immune response / adenyl deoxyribonucleotide binding / activation of immune response / DNA synthesis involved in UV-damage excision repair / atrial cardiac muscle tissue development / lymphoid progenitor cell differentiation / retrotransposition ...immune response in brain or nervous system / immune complex formation / T cell antigen processing and presentation / organ or tissue specific immune response / adenyl deoxyribonucleotide binding / activation of immune response / DNA synthesis involved in UV-damage excision repair / atrial cardiac muscle tissue development / lymphoid progenitor cell differentiation / retrotransposition / MutSalpha complex binding / regulation of catalytic activity / DNA exonuclease activity / DNA modification / regulation of immunoglobulin production / cellular response to hydroxyurea / regulation of lipid biosynthetic process / oligosaccharyltransferase complex / regulation of lysosome organization / regulation of cellular respiration / regulation of fatty acid metabolic process / regulation of protein complex stability / exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / regulation of type I interferon production / inflammatory response to antigenic stimulus / regulation of tumor necrosis factor production / heart process / regulation of T cell activation / MutLalpha complex binding / 3'-5'-DNA exonuclease activity / macrophage activation involved in immune response / glycoprotein biosynthetic process / DNA catabolic process / apoptotic cell clearance / negative regulation of type I interferon-mediated signaling pathway / regulation of glycolytic process / DNA binding, bending / blood vessel development / cellular response to type I interferon / type I interferon-mediated signaling pathway / cGAS/STING signaling pathway / WW domain binding / regulation of innate immune response / DNA metabolic process / negative regulation of cGAS/STING signaling pathway / nuclear replication fork / heart morphogenesis / response to UV / cellular response to interferon-beta / determination of adult lifespan / kidney development / mitotic G1 DNA damage checkpoint signaling / 3'-5' exonuclease activity / DNA damage checkpoint signaling / negative regulation of innate immune response / generation of precursor metabolites and energy / establishment of protein localization / cellular response to reactive oxygen species / cellular response to gamma radiation / protein-DNA complex / cellular response to UV / single-stranded DNA binding / regulation of gene expression / cellular response to oxidative stress / regulation of inflammatory response / double-stranded DNA binding / defense response to virus / adaptive immune response / DNA replication / protein stabilization / immune response / inflammatory response / innate immune response / DNA damage response / endoplasmic reticulum membrane / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / DNA binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Three-prime repair exonuclease 1/2 / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
: / AMMONIUM ION / Three-prime repair exonuclease 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHsiao, Y.Y. / Huang, K.W. / Wu, C.Y. / Tsai, C.Y. / Wu, M.T.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)NSTC 112-2636-B-A49-004 - Taiwan
Ministry of Science and Technology (MoST, Taiwan)NSTC 112-2628-B-A49 -008 -MY3 Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2026
Title: Disordered DNA-binding motif forms a modulation site for inhibiting the cancer immunotherapy target TREX1.
Authors: Huang, K.W. / Yu Tsai, C. / Wu, C.Y. / Lin, W.C. / Wu, M.T. / Hsu, K.C. / Yu Yang, C. / Chang, I.Y. / Liu, H.M. / Chu, J.W. / Hsiao, Y.Y.
History
DepositionNov 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Three-prime repair exonuclease 1
A: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,67419
Polymers54,8942
Non-polymers1,78017
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-86 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.060, 83.082, 87.997
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Three-prime repair exonuclease 1 / 3'-5' exonuclease TREX1


Mass: 27447.154 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 365 molecules

#2: Chemical ChemComp-A1L5Z / 4-oxidanyl-6-[(8-oxidanyl-6-sulfo-naphthalen-2-yl)carbamoylamino]naphthalene-2-sulfonic acid / NSC-37204


Mass: 504.490 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H16N2O9S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H4N
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.085M HEPES sodium pH 7.5, 1.7% v/v Polyethylene glycol 400, 1.7M Ammonium sulfate, 15% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99987 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 61471 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.021 / Rrim(I) all: 0.054 / Χ2: 1.095 / Net I/σ(I): 12.2 / Num. measured all: 425048
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.7-1.767.30.34760740.960.990.1360.3730.484100
1.76-1.837.10.23760490.9790.9950.0950.2560.52100
1.83-1.916.60.16360670.9890.9970.0680.1770.603100
1.91-2.027.20.11960990.9940.9980.0470.1280.694100
2.02-2.146.70.08860860.9960.9990.0370.0960.879100
2.14-2.317.30.07261350.9970.9990.0280.0771.083100
2.31-2.547.30.06261200.9970.9990.0250.0661.376100
2.54-2.917.10.05361700.9980.9990.0210.0581.756100
2.91-3.666.40.04262350.99810.0180.0452.018100
3.66-306.10.0364360.99910.0130.0331.64199.6

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
PHENIX(1.19.2_4158: ???)refinement
PDB_EXTRACTV4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→24.25 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 14.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1709 4641 7.56 %
Rwork0.1503 --
obs0.1518 61403 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→24.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3511 0 109 348 3968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113773
X-RAY DIFFRACTIONf_angle_d1.2395159
X-RAY DIFFRACTIONf_dihedral_angle_d8.495529
X-RAY DIFFRACTIONf_chiral_restr0.065575
X-RAY DIFFRACTIONf_plane_restr0.012665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.19441620.17281734X-RAY DIFFRACTION93
1.72-1.740.18831590.1671842X-RAY DIFFRACTION100
1.74-1.760.21421700.16421874X-RAY DIFFRACTION100
1.76-1.790.18931580.15351862X-RAY DIFFRACTION100
1.79-1.810.19061450.15241888X-RAY DIFFRACTION100
1.81-1.840.1991450.15521873X-RAY DIFFRACTION100
1.84-1.860.1831470.16071876X-RAY DIFFRACTION100
1.86-1.890.2011550.16221858X-RAY DIFFRACTION100
1.89-1.920.17321400.15441899X-RAY DIFFRACTION100
1.92-1.950.15011660.1481880X-RAY DIFFRACTION100
1.95-1.980.19481490.15051887X-RAY DIFFRACTION100
1.98-2.020.18261390.14321876X-RAY DIFFRACTION100
2.02-2.060.15671350.14191891X-RAY DIFFRACTION100
2.06-2.10.1671610.13921882X-RAY DIFFRACTION100
2.1-2.150.15221300.13751908X-RAY DIFFRACTION100
2.15-2.20.14761630.14441891X-RAY DIFFRACTION100
2.2-2.250.17481680.1441867X-RAY DIFFRACTION100
2.25-2.310.17751670.13581885X-RAY DIFFRACTION100
2.31-2.380.15471230.13531922X-RAY DIFFRACTION100
2.38-2.460.14391760.13741870X-RAY DIFFRACTION100
2.46-2.540.1541370.13831911X-RAY DIFFRACTION100
2.54-2.650.14441640.14371877X-RAY DIFFRACTION100
2.65-2.770.18291790.1481883X-RAY DIFFRACTION100
2.77-2.910.15751520.15311914X-RAY DIFFRACTION100
2.91-3.090.17841580.14781908X-RAY DIFFRACTION100
3.09-3.330.16961430.15461930X-RAY DIFFRACTION100
3.33-3.670.18921850.15541913X-RAY DIFFRACTION100
3.67-4.190.14211540.13251936X-RAY DIFFRACTION100
4.2-5.280.16171480.13741975X-RAY DIFFRACTION100
5.28-24.250.21281630.20232050X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 15.8662 Å / Origin y: -8.4522 Å / Origin z: 20.2334 Å
111213212223313233
T0.1044 Å2-0.0117 Å2-0.0015 Å2-0.161 Å2-0.0059 Å2--0.1593 Å2
L0.5137 °20.2299 °2-0.0982 °2-1.5554 °2-0.3578 °2--0.9885 °2
S-0.007 Å °-0.0229 Å °-0.0361 Å °0.0336 Å °-0.0511 Å °-0.2194 Å °0.0075 Å °0.1023 Å °0.0309 Å °
Refinement TLS groupSelection details: all

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