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- PDB-9l8d: Structure of frog TREX1-DNA complex -

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Basic information

Entry
Database: PDB / ID: 9l8d
TitleStructure of frog TREX1-DNA complex
Components
  • DNA (5'-D(*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 / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesRanitomeya imitator (mimic poison frog)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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: DNA (5'-D(*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)32,9183
Polymers32,8932
Non-polymers241
Water1,36976
1
A: Three-prime repair exonuclease 1
B: DNA (5'-D(*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

A: Three-prime repair exonuclease 1
B: DNA (5'-D(*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)65,8356
Polymers65,7874
Non-polymers492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_554y,x,-z-11
Buried area7350 Å2
ΔGint-30 kcal/mol
Surface area23460 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-14 kcal/mol
Surface area13430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.684, 144.684, 82.201
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-361-

HOH

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Components

#1: Protein Three-prime repair exonuclease 1


Mass: 26182.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ranitomeya imitator (mimic poison frog)
Gene: RiTREX1 / Production host: Escherichia coli (E. coli) / References: exodeoxyribonuclease III
#2: DNA chain DNA (5'-D(*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.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 3.27 Å3/Da / Density % sol: 62.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Citric acid pH 4.0, 20% PEG 6000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97849 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97849 Å / Relative weight: 1
ReflectionResolution: 2.03→36.17 Å / Num. obs: 28440 / % possible obs: 99.89 % / Redundancy: 31.9 % / Biso Wilson estimate: 41.19 Å2 / CC1/2: 0.981 / Rpim(I) all: 0.019 / Net I/σ(I): 16.9
Reflection shellResolution: 2.03→2.1 Å / Redundancy: 32.5 % / Mean I/σ(I) obs: 3.35 / Num. unique obs: 2788 / CC1/2: 0.507 / Rpim(I) all: 0.174 / % possible all: 99.25

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5127refinement
xia2data scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7TQN

7tqn


Resolution: 2.03→36.17 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2293 1377 4.84 %
Rwork0.2022 --
obs0.2034 28428 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.03→36.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1711 385 1 76 2173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032181
X-RAY DIFFRACTIONf_angle_d0.6383044
X-RAY DIFFRACTIONf_dihedral_angle_d20.851832
X-RAY DIFFRACTIONf_chiral_restr0.039350
X-RAY DIFFRACTIONf_plane_restr0.004327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.10.37031190.36212669X-RAY DIFFRACTION99
2.1-2.190.31171410.31842666X-RAY DIFFRACTION100
2.19-2.290.29691360.27582660X-RAY DIFFRACTION100
2.29-2.410.25671460.25522666X-RAY DIFFRACTION100
2.41-2.560.24191450.22692672X-RAY DIFFRACTION100
2.56-2.750.25181180.22962697X-RAY DIFFRACTION100
2.75-3.030.21891540.21152683X-RAY DIFFRACTION100
3.03-3.470.24151470.20512721X-RAY DIFFRACTION100
3.47-4.370.20291400.16362735X-RAY DIFFRACTION100
4.37-36.170.20351310.17392882X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4794-0.8817-0.35074.88720.0382.51120.0215-0.246-0.08320.4675-0.19040.1670.136-0.19910.21390.4152-0.0640.10720.37490.02650.352-10.9566-12.5855-27.2884
24.97365.5237-2.32586.7072-2.76371.52040.1644-0.7861-0.07070.8894-0.17020.8813-0.0804-0.2686-0.07760.6071-0.0240.20060.7422-0.00160.9138-30.5701-15.4344-29.7508
32.9164-0.62650.18614.85550.83031.3242-0.05050.0002-0.3739-0.0893-0.0491-0.38610.16880.02040.10640.39360.00630.06630.33710.06110.355-1.7533-17.4242-38.2345
44.91110.12230.44152.65130.35031.1213-0.1064-0.6215-0.21580.5151-0.1299-0.43770.2081-0.05620.22580.5284-0.03120.01910.42960.06170.3027-3.9519-10.702-25.7188
52.24980.6267-0.56883.3158-0.63993.5191-0.0622-0.4294-0.27830.8404-0.040.53120.1758-0.29550.08880.5332-0.03320.19830.48920.040.5017-17.3111-18.1669-21.9378
67.6179-2.0673-0.29115.00181.50527.5137-0.295-1.3877-0.4411.3063-0.13480.68930.3141-0.22320.1971.0954-0.25950.10620.73530.05810.5843-5.4207-28.1385-9.6281
74.2419-1.0968-1.89622.27322.03425.54470.5097-1.3796-0.10191.76160.22920.09090.87740.1522-0.60851.4125-0.22920.03150.81520.05950.5931-6.7456-29.8405-10.4102
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 114 )
4X-RAY DIFFRACTION4chain 'A' and (resid 115 through 150 )
5X-RAY DIFFRACTION5chain 'A' and (resid 151 through 234 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 13 )
7X-RAY DIFFRACTION7chain 'B' and (resid 14 through 22 )

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