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- PDB-9kjs: The mTREX1-NSC 37215 complex structure by co-crystallization (NSC... -

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Basic information

Entry
Database: PDB / ID: 9kjs
TitleThe mTREX1-NSC 37215 complex structure by co-crystallization (NSC 37215-2 Complex 3)
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
: / FORMIC ACID / 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
A: Three-prime repair exonuclease 1
B: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4275
Polymers54,8942
Non-polymers5333
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-7 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.795, 83.913, 88.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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
#2: Chemical ChemComp-A1L50 / 7-[(4-benzamidophenyl)carbonylamino]-4-oxidanyl-naphthalene-2-sulfonic acid / NSC-37215


Mass: 462.475 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H18N2O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O
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: 2.7 Å3/Da / Density % sol: 54.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 35% v/v Tacsimate TM pH 7.0

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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: Mar 3, 2023
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: 62095 / % possible obs: 98.2 % / Redundancy: 8.5 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.019 / Rrim(I) all: 0.055 / Χ2: 0.959 / Net I/σ(I): 12.1 / Num. measured all: 527219
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.7-1.7690.49362220.9290.9810.1710.5220.434100
1.76-1.839.10.33362580.9660.9910.1160.3530.456100
1.83-1.9180.26761860.9710.9930.0990.2860.60999
1.91-2.028.70.18562440.9860.9970.0660.1970.939100
2.02-2.148.20.10262790.9950.9990.0380.1090.627100
2.14-2.317.40.09153680.9930.9980.0360.0981.1285.4
2.31-2.548.50.0663180.99810.0220.0640.902100
2.54-2.9190.04963320.99910.0170.0521.168100
2.91-3.668.40.0462680.99910.0150.0431.67797.8
3.66-308.40.03466200.99910.0130.0371.69699.7

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTV4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→26.67 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.195 4679 7.63 %
Rwork0.169 --
obs0.171 61310 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→26.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 36 460 3991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113655
X-RAY DIFFRACTIONf_angle_d1.2044996
X-RAY DIFFRACTIONf_dihedral_angle_d7.004499
X-RAY DIFFRACTIONf_chiral_restr0.061565
X-RAY DIFFRACTIONf_plane_restr0.014650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.29921490.24021929X-RAY DIFFRACTION100
1.72-1.740.25741430.22281894X-RAY DIFFRACTION99
1.74-1.760.23821500.20721892X-RAY DIFFRACTION100
1.76-1.780.24061660.19851897X-RAY DIFFRACTION100
1.78-1.810.20811720.18271901X-RAY DIFFRACTION100
1.81-1.830.21731500.17731879X-RAY DIFFRACTION100
1.83-1.860.18641630.18181922X-RAY DIFFRACTION100
1.86-1.890.26171750.19391900X-RAY DIFFRACTION100
1.89-1.910.36011440.37631823X-RAY DIFFRACTION95
1.91-1.950.38371420.35441776X-RAY DIFFRACTION92
1.95-1.980.21411590.18321885X-RAY DIFFRACTION100
1.98-2.020.19441610.16731919X-RAY DIFFRACTION100
2.02-2.050.19151680.16751902X-RAY DIFFRACTION100
2.05-2.10.20971720.16041904X-RAY DIFFRACTION100
2.1-2.140.19141650.14371918X-RAY DIFFRACTION100
2.14-2.190.17611460.15571915X-RAY DIFFRACTION100
2.19-2.250.2631190.24581484X-RAY DIFFRACTION77
2.25-2.310.25151120.22481490X-RAY DIFFRACTION77
2.31-2.370.17471300.14731952X-RAY DIFFRACTION100
2.37-2.450.19031340.15131952X-RAY DIFFRACTION100
2.45-2.540.19381680.15121924X-RAY DIFFRACTION100
2.54-2.640.17941620.15481929X-RAY DIFFRACTION100
2.64-2.760.20111450.16261958X-RAY DIFFRACTION100
2.76-2.910.19611590.1641940X-RAY DIFFRACTION100
2.91-3.090.18471730.16061926X-RAY DIFFRACTION100
3.09-3.330.20571770.15881952X-RAY DIFFRACTION100
3.33-3.660.15031480.15291842X-RAY DIFFRACTION94
3.66-4.190.13641860.13681951X-RAY DIFFRACTION100
4.19-5.270.15251470.13022012X-RAY DIFFRACTION100
5.27-26.670.21961940.18392063X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 15.6634 Å / Origin y: -8.87 Å / Origin z: 20.3418 Å
111213212223313233
T0.1041 Å2-0.0126 Å2-0.0187 Å2-0.1388 Å2-0.0123 Å2--0.1308 Å2
L0.7617 °20.093 °2-0.1872 °2-1.5817 °2-0.4258 °2--1.0791 °2
S0.0067 Å °-0.0519 Å °-0.0244 Å °0.0688 Å °-0.0603 Å °-0.1755 Å °0.0176 Å °0.0821 Å °0.027 Å °
Refinement TLS groupSelection details: all

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