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- PDB-9o0w: Co-crystal structure of human TREX1 in complex with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 9o0w
TitleCo-crystal structure of human TREX1 in complex with an inhibitor
ComponentsThree-prime repair exonuclease 1
KeywordsHYDROLASE/INHIBITOR / TREX1 / SGC / TRANSPORT PROTEIN / Structural Genomics / PSI-Biology / Structural Genomics Consortium / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


Regulation by TREX1 / immune response in brain or nervous system / adenyl deoxyribonucleotide binding / immune complex formation / activation of 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 ...Regulation by TREX1 / immune response in brain or nervous system / adenyl deoxyribonucleotide binding / immune complex formation / activation of 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 modification / regulation of lipid biosynthetic process / oligosaccharyltransferase complex / regulation of fatty acid metabolic process / heart process / regulation of protein complex stability / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / lymphoid progenitor cell differentiation / regulation of type I interferon production / cellular response to hydroxyurea / regulation of lysosome organization / 3'-5'-DNA exonuclease activity / regulation of cellular respiration / MutLalpha complex binding / regulation of tumor necrosis factor production / inflammatory response to antigenic stimulus / macrophage activation involved in immune response / DNA catabolic process / IRF3-mediated induction of type I IFN / regulation of immunoglobulin production / regulation of T cell activation / apoptotic cell clearance / regulation of glycolytic process / negative regulation of type I interferon-mediated signaling pathway / DNA binding, bending / DNA metabolic process / WW domain binding / type I interferon-mediated signaling pathway / negative regulation of cGAS/STING signaling pathway / blood vessel development / nuclear replication fork / mismatch repair / heart morphogenesis / cellular response to interferon-beta / mitotic G1 DNA damage checkpoint signaling / 3'-5' exonuclease activity / negative regulation of innate immune response / determination of adult lifespan / generation of precursor metabolites and energy / cellular response to reactive oxygen species / kidney development / establishment of protein localization / cellular response to gamma radiation / protein-DNA complex / nuclear envelope / single-stranded DNA binding / regulation of inflammatory response / double-stranded DNA binding / DNA recombination / defense response to virus / DNA replication / protein stabilization / DNA repair / endoplasmic reticulum membrane / magnesium ion binding / protein homodimerization activity / metal ion binding / 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
: / Three-prime repair exonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsDehghani-Tafti, S. / Dong, A. / Li, Y. / Ackloo, S. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To be published
Title: Co-crystal structure of human TREX1 in complex with an inhibitor
Authors: Dehghani-Tafti, S. / Dong, A. / Li, Y. / Ackloo, S. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionApr 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: 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
C: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,24723
Polymers75,5103
Non-polymers1,73720
Water9,854547
1
A: Three-prime repair exonuclease 1
hetero molecules

A: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,41518
Polymers50,3402
Non-polymers1,07516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3950 Å2
ΔGint-14 kcal/mol
Surface area17350 Å2
MethodPISA
2
B: Three-prime repair exonuclease 1
C: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,53914
Polymers50,3402
Non-polymers1,19912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-12 kcal/mol
Surface area16970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.698, 153.693, 137.471
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-505-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 25169.863 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TREX1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NSU2, exodeoxyribonuclease III

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Non-polymers , 5 types, 567 molecules

#2: Chemical ChemComp-A1B7V / 5-({N-[(2,3-dichlorophenyl)methyl]-3,5-difluorobenzamido}methyl)pyridine-2-carboxylic acid


Mass: 451.250 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H14Cl2F2N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 9 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / 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: 2.75 Å3/Da / Density % sol: 55.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200mM KBr, 8% PEG 20K, 8% PEG 550 MME, 100mM Tris [pH 7.5]

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.43→50 Å / Num. obs: 152888 / % possible obs: 99.9 % / Redundancy: 8.4 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.024 / Rrim(I) all: 0.069 / Χ2: 0.806 / Net I/σ(I): 8.1 / Num. measured all: 1281588
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.43-1.458.50.93575500.7570.9280.3370.9950.632100
1.45-1.488.50.76976150.8350.9540.2750.8170.64199.9
1.48-1.518.40.63275830.8670.9640.2290.6730.657100
1.51-1.548.40.5475980.8970.9720.1960.5750.662100
1.54-1.578.30.4575830.9260.9810.1640.4790.681100
1.57-1.618.10.37575700.9470.9860.1390.40.68799.9
1.61-1.657.40.30975850.9560.9890.120.3320.702100
1.65-1.78.20.26276060.9720.9930.0970.280.722100
1.7-1.758.80.21376140.9830.9960.0760.2260.742100
1.75-1.88.80.17776180.9890.9970.0630.1870.744100
1.8-1.878.70.13576180.9930.9980.0480.1440.768100
1.87-1.948.60.11275700.9940.9990.040.120.79100
1.94-2.038.50.09176770.9960.9990.0330.0970.824100
2.03-2.148.30.07476310.9970.9990.0270.0790.85899.9
2.14-2.277.70.0676650.9980.9990.0230.0650.88199.9
2.27-2.458.20.05276310.99810.0190.0560.901100
2.45-2.6990.04877150.99910.0170.0510.959100
2.69-3.088.90.04277090.99910.0150.0451.062100
3.08-3.888.40.03677550.99910.0130.0381.127100
3.88-5080.03279950.99910.0120.0341.04399.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→49.11 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.792 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18123 3070 2 %RANDOM
Rwork0.16156 ---
obs0.16195 149775 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.512 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-0 Å2
2--0.06 Å20 Å2
3----0.26 Å2
Refinement stepCycle: 1 / Resolution: 1.43→49.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4796 0 122 547 5465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0125321
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164953
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.817305
X-RAY DIFFRACTIONr_angle_other_deg0.4891.72911434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8245689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.124534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16910770
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.2822
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026532
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021164
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.481.8442699
X-RAY DIFFRACTIONr_mcbond_other3.4791.8442699
X-RAY DIFFRACTIONr_mcangle_it5.6333.2893404
X-RAY DIFFRACTIONr_mcangle_other5.6333.293405
X-RAY DIFFRACTIONr_scbond_it3.5351.9912622
X-RAY DIFFRACTIONr_scbond_other3.5351.9922623
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.573.5993901
X-RAY DIFFRACTIONr_long_range_B_refined11.14220.125915
X-RAY DIFFRACTIONr_long_range_B_other10.1818.25737
X-RAY DIFFRACTIONr_rigid_bond_restr2.06310274
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.43→1.466 Å
RfactorNum. reflection% reflection
Rfree0.261 234 -
Rwork0.224 10619 -
obs--96.19 %

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