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- PDB-9l88: Structure of human TREX1-DNA complex with K66R disease-associated... -

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Basic information

Entry
Database: PDB / ID: 9l88
TitleStructure of human TREX1-DNA complex with K66R disease-associated mutation
Components
  • DNA (5'-D(P*GP*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*AP*TP*C)-3')
  • Three-prime repair exonuclease 1
KeywordsIMMUNE SYSTEM/DNA / nuclease / DNase / innate immunity / autoimmunity / cancer / IMMUNE SYSTEM-DNA complex
Function / homology
Function and homology information


Regulation by TREX1 / adenyl deoxyribonucleotide binding / MutSalpha complex binding / oligosaccharyltransferase complex / exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / MutLalpha complex binding / 3'-5'-DNA exonuclease activity / IRF3-mediated induction of type I IFN / DNA catabolic process ...Regulation by TREX1 / adenyl deoxyribonucleotide binding / MutSalpha complex binding / oligosaccharyltransferase complex / exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / MutLalpha complex binding / 3'-5'-DNA exonuclease activity / IRF3-mediated induction of type I IFN / DNA catabolic process / DNA binding, bending / WW domain binding / DNA metabolic process / negative regulation of cGAS/STING signaling pathway / nuclear replication fork / mismatch repair / 3'-5' exonuclease activity / negative regulation of innate immune response / protein-DNA complex / nuclear envelope / single-stranded DNA binding / double-stranded DNA binding / DNA recombination / DNA replication / 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
: / DNA / DNA (> 10) / Three-prime repair exonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsZhu, J. / Wang, L. / Lin, C. / Zhou, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270920 China
CitationJournal: Immunity / Year: 2026
Title: Distinct recognition pattern for double-stranded DNA allows TREX1 to maintain immune homeostasis
Authors: Zhu, J. / Wang, L. / Lin, C. / Zhou, W.
History
DepositionDec 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 29, 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
C: DNA (5'-D(P*GP*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*AP*TP*C)-3')
D: DNA (5'-D(P*GP*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*AP*TP*C)-3')
E: Three-prime repair exonuclease 1
F: Three-prime repair exonuclease 1
G: DNA (5'-D(P*GP*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*AP*TP*C)-3')
H: DNA (5'-D(P*GP*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*AP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,89110
Polymers130,8778
Non-polymers142
Water4,017223
1
A: Three-prime repair exonuclease 1
B: Three-prime repair exonuclease 1
C: DNA (5'-D(P*GP*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*AP*TP*C)-3')
D: DNA (5'-D(P*GP*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*AP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4455
Polymers65,4384
Non-polymers71
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-18 kcal/mol
Surface area21620 Å2
MethodPISA
2
E: Three-prime repair exonuclease 1
F: Three-prime repair exonuclease 1
G: DNA (5'-D(P*GP*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*AP*TP*C)-3')
H: DNA (5'-D(P*GP*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*AP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4455
Polymers65,4384
Non-polymers71
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-16 kcal/mol
Surface area21220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.257, 92.712, 160.551
Angle α, β, γ (deg.)90.00, 90.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 26008.924 Da / Num. of mol.: 4 / Mutation: K66R
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
#2: DNA chain
DNA (5'-D(P*GP*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*AP*TP*C)-3')


Mass: 6710.313 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.05 M Li2SO4, 22.5% PEG-3350, 0.1M Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.62→32.22 Å / Num. obs: 38765 / % possible obs: 99.34 % / Redundancy: 8.3 % / Biso Wilson estimate: 33.61 Å2 / CC1/2: 0.976 / Rpim(I) all: 0.07 / Net I/σ(I): 11.3
Reflection shellResolution: 2.62→2.69 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3673 / CC1/2: 0.717 / Rpim(I) all: 0.322 / % possible all: 93.33

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5127refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7TQQ
Resolution: 2.62→32.22 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2318 2000 5.16 %
Rwork0.1946 --
obs0.1965 38765 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.99 Å2
Refinement stepCycle: LAST / Resolution: 2.62→32.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6510 1223 2 223 7958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048046
X-RAY DIFFRACTIONf_angle_d0.69611209
X-RAY DIFFRACTIONf_dihedral_angle_d20.4323029
X-RAY DIFFRACTIONf_chiral_restr0.0421284
X-RAY DIFFRACTIONf_plane_restr0.0051243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.690.2551350.22972427X-RAY DIFFRACTION93
2.69-2.760.26391400.23052656X-RAY DIFFRACTION99
2.76-2.840.28581470.24312582X-RAY DIFFRACTION100
2.84-2.930.29871390.23382651X-RAY DIFFRACTION99
2.93-3.040.30421410.22852606X-RAY DIFFRACTION100
3.04-3.160.25591440.20822640X-RAY DIFFRACTION100
3.16-3.30.22521430.20892614X-RAY DIFFRACTION100
3.3-3.480.25591420.20952612X-RAY DIFFRACTION100
3.48-3.70.25611480.19442682X-RAY DIFFRACTION100
3.7-3.980.24781360.17732628X-RAY DIFFRACTION100
3.98-4.380.191470.1632648X-RAY DIFFRACTION100
4.38-5.010.1811500.15572634X-RAY DIFFRACTION100
5.01-6.30.18661520.18512669X-RAY DIFFRACTION100
6.31-32.220.21761360.19262716X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.21-0.17380.52690.2620.02810.8384-0.0367-0.14460.09520.7045-0.02270.1252-0.2476-0.0532-0.00140.3946-0.02740.04780.291-0.02640.38054.455627.9252-55.3036
20.0670.1204-0.48182.12690.37611.1812-0.0309-0.1696-0.03730.2828-0.0199-0.2019-0.00160.27740.12020.2522-0.022-0.03720.33120.01760.31939.606920.121-56.6586
30.908-0.0784-0.44661.5389-0.40971.26750.0516-0.43470.0250.70350.02560.1495-0.0419-0.13270.0460.5296-0.00040.0130.3491-0.05940.19570.669626.8177-47.9617
40.38910.0312-0.12150.8933-0.98550.6841-0.2221-0.1247-0.0242-0.34590.289-0.10450.08570.18580.32380.1786-0.04480.03740.2757-0.01460.38621.699121.625-81.6996
50.1695-0.5274-0.09570.3829-0.44010.26210.0475-0.17380.0771-0.1989-0.18270.2762-0.01310.1472-0.23110.2132-0.0568-0.00080.19430.03220.32820.233329.0325-78.924
61.4405-0.56680.67910.74940.27950.9362-0.3562-0.4943-0.463-0.31520.13110.27690.1767-0.3028-0.27430.288-0.1420.05990.2726-0.03340.2754-7.001717.4085-69.8544
70.27710.52860.35760.8091-0.3440.7953-0.12460.0298-0.03450.4114-0.0478-0.1328-0.08710.1524-0.00050.2575-0.0151-00.27-0.00250.31796.211737.8751-72.3547
80.34140.1072-0.20020.27380.18820.5715-0.00390.3325-0.068-0.1495-0.27070.37240.19450.2358-0.16510.24890.04260.0330.25450.04560.3821.447124.4491-83.8447
90.4249-0.08550.88790.2506-0.10651.7034-0.46590.2169-0.3466-0.23180.2295-0.4268-0.2970.415-0.25610.18760.02460.12460.2389-0.02180.317710.566331.863-84.8064
100.01310.1439-0.10290.911-0.81590.76470.39010.7904-0.6915-0.8603-0.338-0.381-0.2723-0.048-0.27820.41730.02580.00790.2749-0.11210.363-8.725222.6091-89.3183
110.13610.24870.27330.7986-0.00580.7569-0.0776-0.11880.17670.16450.02790.4958-0.1497-0.3114-0.01840.1909-0.00860.04820.23210.00440.3492-13.693827.3968-77.4412
120.8831-0.37380.26180.2096-0.0940.2736-0.08980.3534-1.0004-0.5634-0.2660.59520.3421-0.67590.07130.3946-0.0564-0.10760.2926-0.11260.4001-8.404814.425-86.0609
130.8757-0.7853-0.01460.6804-0.01180.0493-0.0347-0.21620.6632-1.0590.1805-0.905-0.0760.2401-0.01770.4486-0.0080.11810.2695-0.02910.39656.352230.9932-91.1194
141.1441-0.7309-0.05030.45770.04560.0042-0.3779-0.0338-1.3850.44890.21580.70221.0983-0.3333-0.05331.33310.0781-0.08261.1105-0.00170.67966.01167.5385-40.2285
150.1440.1867-0.06420.1387-0.03620.09010.8749-1.3469-0.6670.24070.4072-0.8243-0.73740.82480.00041.3509-0.1104-0.07141.5060.0630.88715.890814.6287-27.1833
161.29210.0928-0.94320.0553-0.12150.76390.97230.16230.42870.52020.60310.13720.7491-0.40130.27670.6922-0.0618-0.03730.3744-0.05620.24580.764212.2479-39.2072
170.9636-0.74570.36073.0332-1.44551.1547-0.0686-0.1528-0.5025-1.6040.48811.16150.6009-0.80591.24590.5042-0.1589-0.31380.294-0.13730.5103-12.341939.4203-93.09
18-0.14990.5374-0.33740.3337-0.25250.9981-0.22420.0958-0.1331-0.07330.1391-0.17180.0345-0.0414-0.00110.25860.0282-0.0180.3294-0.03530.3394-15.0178-14.3025-25.2061
190.2321-0.229-0.07180.22040.25140.6396-0.0863-0.23630.5067-0.24480.0458-0.2783-0.177-0.0004-0.00970.2301-0.0521-0.01510.27580.10930.3867-4.94290.5128-16.8793
200.24160.3949-0.07060.72780.04080.9194-0.03660.0051-0.09520.3229-0.11660.06610.06840.0603-0.01940.2204-0.02160.03710.2160.01230.2467-19.9044-23.3858-17.4217
210.22110.12780.06951.13131.141.6865-0.06150.45010.0604-0.9962-0.18240.0697-0.9003-0.3317-0.17830.2442-0.0780.08240.43440.06870.198-15.632-11.3825-29.4446
220.8381-0.3010.05930.4969-0.48880.48180.08020.41140.4885-0.52950.02590.11610.122-0.13280.01880.3235-0.0554-0.02380.4089-0.03410.1844-17.4756-15.2761-32.0168
23-0.00880.01710.00950.28050.0057-0.0063-0.24040.1839-0.3784-0.42560.4761-0.74820.13070.1651-0.00010.3623-0.07030.07790.3468-0.02240.37283.6803-13.4312-29.5417
240.2999-0.0902-0.03070.5242-0.2980.5696-0.08350.1788-0.2928-0.1472-0.0503-0.77160.33530.41290.0020.3020.02670.00870.43310.0280.3012-3.6439-14.7828-19.2825
250.2531-0.0746-0.09070.10660.16110.1335-0.04470.48010.134-0.4882-0.0933-0.1537-0.02540.44920.03630.4156-0.06120.01490.39630.11870.3536-6.1221-1.1358-31.5557
260.5672-0.1094-0.30290.02830.08150.14640.10760.14270.0055-0.75970.19030.47250.769-0.5313-0.01430.5385-0.0628-0.1710.4182-0.04360.2-20.3066-18.1688-36.6932
270.0623-0.07210.00620.2978-0.10580.74130.0720.13150.08530.0989-0.0844-0.00590.0869-0.084-0.00920.2545-0.0015-0.01120.25040.01920.3701-21.661-12.01080.0481
280.11350.08560.11990.4061-0.31891.1444-0.2397-0.8728-0.05540.0760.49860.07160.4794-0.37870.03730.37430.1427-0.09870.39430.00350.3269-7.2122-24.6399-3.1971
29-0.05-0.1613-0.26281.34460.31340.33380.0220.17840.0734-0.1305-0.084-0.0273-0.1507-0.0616-0.17480.13030.0191-0.01730.20540.02870.2353-22.7632-5.099-6.3569
300.1705-0.04040.29910.0902-0.15390.0784-0.2867-0.2547-0.40290.40810.0622-0.0131-0.2737-0.40620.00110.2909-0.00340.02640.32690.05710.3815-32.6044-6.6604-0.5359
310.72370.6315-0.21141.32080.02580.56980.3959-0.00970.02760.8513-0.1680.59890.57520.48540.25380.8587-0.015-0.11930.2423-0.04550.2146-18.2553-15.605911.7916
320.61330.0497-0.10450.01020.20410.8434-0.6904-0.6502-0.39711.52940.302-0.85480.72590.6899-0.2124-0.43640.4631-1.05420.25580.2278-0.0802-7.0194-12.437212.178
330.03790.0580.02890.08290.05080.0512-0.229-0.0159-0.03330.6949-0.5581-0.1441-0.51520.61750.00030.35570.06010.0110.73960.07940.6125-4.9732-6.59490.0125
340.8558-0.49650.55950.3494-0.06611.70130.1482-0.3308-0.48250.9219-0.0451-0.25980.130.41190.28740.41760.011-0.0420.24970.04830.3178-14.3472-19.39835.7706
350.058-0.0493-0.03460.03320.05030.02930.13540.362-0.13360.7999-0.06020.7592-0.102-0.0475-0.01250.3284-0.02720.05730.3670.04130.4641-32.0676-7.62216.8268
361.33231.14792.90372.76071.91027.5016-0.34221.7497-0.3657-0.10371.3942-1.14421.89730.88751.30120.4847-0.1010.25691.01410.07610.5025-2.6835-27.8444-38.1465
370.8876-0.140.24550.35630.39761.0664-0.0249-0.4787-0.18941.56160.4498-0.40580.40970.70030.67390.97450.1354-0.05540.40590.08130.2309-18.85740.482617.6703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 64 )
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 165 )
3X-RAY DIFFRACTION3chain 'A' and (resid 166 through 234 )
4X-RAY DIFFRACTION4chain 'B' and (resid 7 through 21 )
5X-RAY DIFFRACTION5chain 'B' and (resid 22 through 45 )
6X-RAY DIFFRACTION6chain 'B' and (resid 46 through 70 )
7X-RAY DIFFRACTION7chain 'B' and (resid 71 through 114 )
8X-RAY DIFFRACTION8chain 'B' and (resid 115 through 129 )
9X-RAY DIFFRACTION9chain 'B' and (resid 130 through 150 )
10X-RAY DIFFRACTION10chain 'B' and (resid 151 through 164 )
11X-RAY DIFFRACTION11chain 'B' and (resid 165 through 208 )
12X-RAY DIFFRACTION12chain 'B' and (resid 209 through 222 )
13X-RAY DIFFRACTION13chain 'B' and (resid 223 through 234 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 5 )
15X-RAY DIFFRACTION15chain 'C' and (resid 6 through 16 )
16X-RAY DIFFRACTION16chain 'C' and (resid 17 through 22 )
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 22 )
18X-RAY DIFFRACTION18chain 'E' and (resid 8 through 44 )
19X-RAY DIFFRACTION19chain 'E' and (resid 45 through 64 )
20X-RAY DIFFRACTION20chain 'E' and (resid 65 through 114 )
21X-RAY DIFFRACTION21chain 'E' and (resid 115 through 129 )
22X-RAY DIFFRACTION22chain 'E' and (resid 130 through 163 )
23X-RAY DIFFRACTION23chain 'E' and (resid 164 through 187 )
24X-RAY DIFFRACTION24chain 'E' and (resid 188 through 208 )
25X-RAY DIFFRACTION25chain 'E' and (resid 209 through 222 )
26X-RAY DIFFRACTION26chain 'E' and (resid 223 through 234 )
27X-RAY DIFFRACTION27chain 'F' and (resid 7 through 45 )
28X-RAY DIFFRACTION28chain 'F' and (resid 46 through 64 )
29X-RAY DIFFRACTION29chain 'F' and (resid 65 through 129 )
30X-RAY DIFFRACTION30chain 'F' and (resid 130 through 150 )
31X-RAY DIFFRACTION31chain 'F' and (resid 151 through 163 )
32X-RAY DIFFRACTION32chain 'F' and (resid 164 through 187 )
33X-RAY DIFFRACTION33chain 'F' and (resid 188 through 196 )
34X-RAY DIFFRACTION34chain 'F' and (resid 197 through 222 )
35X-RAY DIFFRACTION35chain 'F' and (resid 223 through 234 )
36X-RAY DIFFRACTION36chain 'G' and (resid 1 through 22 )
37X-RAY DIFFRACTION37chain 'H' and (resid 1 through 22 )

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