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- PDB-9kjg: The mTREX1-NSC 37203 complex structure by co-crystallization (NSC... -

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Basic information

Entry
Database: PDB / ID: 9kjg
TitleThe mTREX1-NSC 37203 complex structure by co-crystallization (NSC 37203 Complex 1)
ComponentsThree-prime repair exonuclease 1
KeywordsHYDROLASE / TREX1 / Inhibitor / DEDDh exonuclease
Function / homology
Function and homology information


cellular response to type I interferon / immune response in brain or nervous system / adenyl deoxyribonucleotide binding / immune complex formation / activation of immune response / organ or tissue specific immune response / DNA synthesis involved in UV-damage excision repair / atrial cardiac muscle tissue development / T cell antigen processing and presentation / MutSalpha complex binding ...cellular response to type I interferon / immune response in brain or nervous system / adenyl deoxyribonucleotide binding / immune complex formation / activation of immune response / organ or tissue specific immune response / DNA synthesis involved in UV-damage excision repair / atrial cardiac muscle tissue development / T cell antigen processing and presentation / MutSalpha complex binding / retrotransposition / DNA exonuclease activity / DNA modification / regulation of lipid biosynthetic process / oligosaccharyltransferase complex / regulation of fatty acid metabolic process / heart process / regulation of protein complex stability / exodeoxyribonuclease III / lymphoid progenitor cell differentiation / double-stranded DNA 3'-5' DNA exonuclease activity / regulation of type I interferon production / regulation of lysosome organization / glycoprotein biosynthetic process / cellular response to hydroxyurea / regulation of tumor necrosis factor production / MutLalpha complex binding / 3'-5'-DNA exonuclease activity / regulation of immunoglobulin production / inflammatory response to antigenic stimulus / macrophage activation involved in immune response / regulation of cellular respiration / DNA catabolic process / regulation of T cell activation / apoptotic cell clearance / regulation of glycolytic process / DNA binding, bending / cGAS/STING signaling pathway / negative regulation of type I interferon-mediated signaling pathway / WW domain binding / regulation of innate immune response / DNA metabolic process / type I interferon-mediated signaling pathway / negative regulation of cGAS/STING signaling pathway / blood vessel development / nuclear replication fork / response to UV / heart morphogenesis / cellular response to interferon-beta / mitotic G1 DNA damage checkpoint signaling / 3'-5' exonuclease activity / negative regulation of innate immune response / DNA damage checkpoint signaling / determination of adult lifespan / generation of precursor metabolites and energy / kidney development / cellular response to reactive oxygen species / establishment of protein localization / 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 / cytoplasm / cytosol
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
: / : / Three-prime repair exonuclease 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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
A: Three-prime repair exonuclease 1
B: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9679
Polymers54,8942
Non-polymers1,0737
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-41 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.488, 83.765, 88.579
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 AB

#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 , 6 types, 328 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-A1L5X / Rhoduline Acid / NSC-37203


Mass: 461.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H15NO8S2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.3M Lithium sulfate, 0.1M Sodium HEPES, pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 44269 / % possible obs: 99.9 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.9-1.977.20.46543330.870.9650.1760.4990.52299.9
1.97-2.057.80.34743680.9390.9840.1270.370.516100
2.05-2.148.10.27243560.9620.990.0970.2890.687100
2.14-2.258.10.22343890.9790.9950.0790.2370.834100
2.25-2.398.40.1643880.990.9970.0560.170.82100
2.39-2.588.90.12844100.9930.9980.0430.1350.94899.9
2.58-2.849.10.144070.9960.9990.0330.1051.18799.9
2.84-3.259.30.07744540.9980.9990.0250.0811.572100
3.25-4.099.20.0644790.99810.020.0631.99899.9
4.09-3090.04946850.99910.0160.0511.84599.8

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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: 1.91→28.73 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1989 3415 7.73 %
Rwork0.1691 --
obs0.1714 44207 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.91→28.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3483 0 66 321 3870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013631
X-RAY DIFFRACTIONf_angle_d0.9374958
X-RAY DIFFRACTIONf_dihedral_angle_d8.726503
X-RAY DIFFRACTIONf_chiral_restr0.053555
X-RAY DIFFRACTIONf_plane_restr0.007638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.930.32521250.28081420X-RAY DIFFRACTION85
1.93-1.960.25761410.23261674X-RAY DIFFRACTION100
1.96-1.990.25991500.20781682X-RAY DIFFRACTION100
1.99-2.030.22631160.18771698X-RAY DIFFRACTION100
2.03-2.060.19641440.17871699X-RAY DIFFRACTION100
2.06-2.10.20451500.1751687X-RAY DIFFRACTION100
2.1-2.140.19831780.1651640X-RAY DIFFRACTION100
2.14-2.180.21181510.16211679X-RAY DIFFRACTION100
2.18-2.230.21851550.17251678X-RAY DIFFRACTION100
2.23-2.280.24991510.19631687X-RAY DIFFRACTION100
2.28-2.340.19441530.16411701X-RAY DIFFRACTION100
2.34-2.40.18621460.15841694X-RAY DIFFRACTION100
2.4-2.470.21531290.15731712X-RAY DIFFRACTION100
2.47-2.550.20181360.16421697X-RAY DIFFRACTION100
2.55-2.640.22771340.16481703X-RAY DIFFRACTION100
2.64-2.750.21371260.17261723X-RAY DIFFRACTION100
2.75-2.870.21191460.17421723X-RAY DIFFRACTION100
2.87-3.020.19261320.17451720X-RAY DIFFRACTION100
3.02-3.210.20181440.17691721X-RAY DIFFRACTION100
3.21-3.460.20441300.16951728X-RAY DIFFRACTION100
3.46-3.810.17791800.15751708X-RAY DIFFRACTION100
3.81-4.360.1621300.13461763X-RAY DIFFRACTION100
4.36-5.480.13911260.14431785X-RAY DIFFRACTION100
5.49-28.730.24881420.2031870X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 16.1395 Å / Origin y: -8.2938 Å / Origin z: 20.1866 Å
111213212223313233
T0.1858 Å2-0.0096 Å2-0.0174 Å2-0.2453 Å2-0.0204 Å2--0.2276 Å2
L0.8013 °20.1841 °2-0.0221 °2-1.9965 °2-0.4729 °2--1.239 °2
S0.0333 Å °-0.025 Å °-0.012 Å °0.0448 Å °-0.0349 Å °-0.129 Å °0.0008 Å °0.0783 Å °-0.0065 Å °
Refinement TLS groupSelection details: all

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