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- PDB-9kjh: The mTREX1-NSC 37203 complex structure by soaking in Soaking Cond... -

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Basic information

Entry
Database: PDB / ID: 9kjh
TitleThe mTREX1-NSC 37203 complex structure by soaking in Soaking Condition 1 (NSC 37203 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
: / ACETATE ION / CACODYLATE ION / Three-prime repair exonuclease 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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)56,03114
Polymers54,8942
Non-polymers1,13712
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-14 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.599, 83.586, 88.780
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 , 7 types, 438 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#5: 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
#6: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.69 Å3/Da / Density % sol: 54.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium cacodylate trihydrate pH 6.5, 1.4M Sodium acetate trihydrate

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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: Aug 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 52801 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.093 / 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
1.8-1.866.90.43752050.8990.9730.180.4740.607100
1.86-1.947.20.33252170.9480.9860.1340.3590.736100
1.94-2.037.30.26951860.9650.9910.1080.290.88100
2.03-2.137.50.21852360.9760.9940.0860.2351.129100
2.13-2.277.70.18752360.9830.9960.0730.2011.336100
2.27-2.447.80.16252510.9870.9970.0630.1741.62100
2.44-2.697.90.1352840.990.9970.050.1391.941100
2.69-3.087.80.10352760.9940.9980.040.112.447100
3.08-3.887.70.0853580.9960.9990.0310.0863.107100
3.88-307.40.06755520.9960.9990.0270.0723.0499.7

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
PHENIX(1.14_3260: ???)refinement
PDB_EXTRACTV4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→28.228 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 16.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1886 3949 7.49 %
Rwork0.165 --
obs0.1667 52691 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→28.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3496 0 69 426 3991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053648
X-RAY DIFFRACTIONf_angle_d0.7744975
X-RAY DIFFRACTIONf_dihedral_angle_d10.6372207
X-RAY DIFFRACTIONf_chiral_restr0.044558
X-RAY DIFFRACTIONf_plane_restr0.005646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8220.23631370.22831658X-RAY DIFFRACTION95
1.822-1.8450.25481330.21731719X-RAY DIFFRACTION100
1.845-1.86930.24431400.20871692X-RAY DIFFRACTION100
1.8693-1.89490.24591220.20221748X-RAY DIFFRACTION100
1.8949-1.9220.21251180.1871726X-RAY DIFFRACTION100
1.922-1.95060.18131420.17461739X-RAY DIFFRACTION100
1.9506-1.98110.2031330.18171733X-RAY DIFFRACTION100
1.9811-2.01360.1981450.17781720X-RAY DIFFRACTION100
2.0136-2.04830.23581350.17511729X-RAY DIFFRACTION100
2.0483-2.08550.20441590.16341701X-RAY DIFFRACTION100
2.0855-2.12560.21011530.16341706X-RAY DIFFRACTION100
2.1256-2.1690.19841490.16191726X-RAY DIFFRACTION100
2.169-2.21610.19011450.171744X-RAY DIFFRACTION100
2.2161-2.26770.17241490.16131701X-RAY DIFFRACTION100
2.2677-2.32440.17981450.15431726X-RAY DIFFRACTION100
2.3244-2.38720.21641380.15831748X-RAY DIFFRACTION100
2.3872-2.45740.17471680.15981700X-RAY DIFFRACTION100
2.4574-2.53660.18461780.1571711X-RAY DIFFRACTION100
2.5366-2.62720.18511450.15121722X-RAY DIFFRACTION100
2.6272-2.73230.17791540.16081718X-RAY DIFFRACTION100
2.7323-2.85660.20271310.17441775X-RAY DIFFRACTION100
2.8566-3.0070.19321280.15911764X-RAY DIFFRACTION100
3.007-3.19520.18181340.15771766X-RAY DIFFRACTION100
3.1952-3.44150.1971340.16351781X-RAY DIFFRACTION100
3.4415-3.78710.15841430.16071771X-RAY DIFFRACTION100
3.7871-4.33340.15981280.141793X-RAY DIFFRACTION100
4.3334-5.45320.17351370.14551815X-RAY DIFFRACTION100
5.4532-28.2280.21571260.2041910X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 15.814 Å / Origin y: -8.197 Å / Origin z: 20.2464 Å
111213212223313233
T0.1161 Å2-0.0092 Å2-0.0089 Å2-0.1613 Å2-0.0037 Å2--0.1371 Å2
L0.7 °20.2656 °2-0.1801 °2-1.5637 °2-0.3516 °2--0.9904 °2
S0.0313 Å °-0.0574 Å °-0.0289 Å °0.0509 Å °-0.0805 Å °-0.128 Å °0.0082 Å °0.1269 Å °0.0291 Å °
Refinement TLS groupSelection details: all

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