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- PDB-8vl7: Co-crystal structure of human TREX1 in complex with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 8vl7
TitleCo-crystal structure of human TREX1 in complex with an inhibitor
ComponentsThree-prime repair exonuclease 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Trex1 / inhibitor / nuclease / SGC / HYDROLASE / HYDROLASE-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 / oligosaccharyltransferase complex / DNA modification / regulation of lipid biosynthetic process / regulation of fatty acid metabolic process / regulation of protein complex stability / heart process / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / cellular response to hydroxyurea / lymphoid progenitor cell differentiation / regulation of type I interferon production / 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 / DNA binding, bending / regulation of glycolytic process / negative regulation of type I interferon-mediated signaling pathway / DNA metabolic process / WW domain binding / negative regulation of cGAS/STING signaling pathway / type I interferon-mediated 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 / cellular response to reactive oxygen species / generation of precursor metabolites and energy / 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 / 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
Chem-A1ACJ / DI(HYDROXYETHYL)ETHER / Three-prime repair exonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsDehghani-Tafti, S. / Dong, A. / Li, Y. / Ackloo, S. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L.
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.
History
DepositionJan 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2024Provider: 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
D: Three-prime repair exonuclease 1
E: Three-prime repair exonuclease 1
F: Three-prime repair exonuclease 1
G: Three-prime repair exonuclease 1
H: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,84741
Polymers200,2628
Non-polymers4,58533
Water8,089449
1
A: Three-prime repair exonuclease 1
B: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,15712
Polymers50,0662
Non-polymers1,09210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-39 kcal/mol
Surface area19150 Å2
MethodPISA
2
C: Three-prime repair exonuclease 1
D: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,36610
Polymers50,0662
Non-polymers1,3008
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-39 kcal/mol
Surface area18270 Å2
MethodPISA
3
E: Three-prime repair exonuclease 1
F: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,25910
Polymers50,0662
Non-polymers1,1948
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-40 kcal/mol
Surface area18710 Å2
MethodPISA
4
G: Three-prime repair exonuclease 1
H: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0659
Polymers50,0662
Non-polymers1,0007
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-39 kcal/mol
Surface area18230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.827, 56.336, 162.853
Angle α, β, γ (deg.)93.12, 98.22, 99.92
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 25032.766 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TREX1 / Plasmid: BL21(DE3)V2R-pRARE2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NSU2, exodeoxyribonuclease III

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Non-polymers , 7 types, 482 molecules

#2: Chemical
ChemComp-A1ACJ / (2P)-2-[3-bromo-2-(2-hydroxyethoxy)phenyl]-5-hydroxy-1-methyl-N-(1,2-oxazol-4-yl)-6-oxo-1,6-dihydropyrimidine-4-carboxamide


Mass: 451.228 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H15BrN4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 300mM MgNO4, 26% PEG 3350, 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-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.88→35 Å / Num. obs: 141898 / % possible obs: 90.6 % / Redundancy: 2 % / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.058 / Rrim(I) all: 0.086 / Χ2: 1.453 / Net I/σ(I): 14.5 / Num. measured all: 285236
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.88-1.9120.59470830.6420.8840.560.8181.31690.7
1.91-1.9520.51472880.7030.9090.4820.7061.29392.4
1.95-1.982.10.42671100.7920.940.3990.5851.32992.2
1.98-2.032.10.3672330.8620.9620.3370.4941.37892.5
2.03-2.072.10.29873120.8720.9650.2790.411.492.3
2.07-2.122.10.24471970.9150.9780.2290.3361.41992.4
2.12-2.172.10.272060.9390.9840.1880.2751.39791.8
2.17-2.232.10.17771810.9460.9860.1660.2431.46391.5
2.23-2.2920.14671060.960.990.1370.21.46791
2.29-2.3720.12371020.9720.9930.1140.1681.45691.1
2.37-2.4520.10770880.9760.9940.0990.1461.49389.8
2.45-2.551.90.08969030.9830.9960.0830.1221.57788.3
2.55-2.671.90.07465270.9870.9970.0690.1021.58283.2
2.67-2.8120.0773150.9880.9970.0640.0951.55493.6
2.81-2.9820.05973930.990.9970.0540.081.51794.3
2.98-3.2120.05472150.9870.9970.050.0741.63492.7
3.21-3.5420.04972690.9890.9970.0450.0671.63392.4
3.54-4.051.90.04568820.9880.9970.0410.0621.48287.9
4.05-5.11.80.04362580.990.9970.0390.0581.45479.6
5.1-352.10.03672300.9950.9990.0310.0471.28692.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→34.64 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.189 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23279 7249 5.1 %RANDOM
Rwork0.19228 ---
obs0.19437 134566 90.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.382 Å2
Baniso -1Baniso -2Baniso -3
1-3.15 Å2-0.61 Å22.23 Å2
2---1.57 Å20.3 Å2
3----1.93 Å2
Refinement stepCycle: 1 / Resolution: 1.88→34.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13130 0 284 449 13863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01313896
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712711
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.64518885
X-RAY DIFFRACTIONr_angle_other_deg1.2121.57329467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.06251751
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.08621.16569
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.326151962
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1251583
X-RAY DIFFRACTIONr_chiral_restr0.060.21790
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216223
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022750
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_it2.5453.827064
X-RAY DIFFRACTIONr_mcbond_other2.5453.827065
X-RAY DIFFRACTIONr_mcangle_it3.685.7078791
X-RAY DIFFRACTIONr_mcangle_other3.685.7078791
X-RAY DIFFRACTIONr_scbond_it2.8384.0686832
X-RAY DIFFRACTIONr_scbond_other2.8374.0686833
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3496.04310095
X-RAY DIFFRACTIONr_long_range_B_refined6.07745.96414683
X-RAY DIFFRACTIONr_long_range_B_other6.07645.96514684
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.927 Å
RfactorNum. reflection% reflection
Rfree0.358 545 -
Rwork0.324 9519 -
obs--86.68 %

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