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- PDB-9l86: Structure of frog TREX1 -

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Basic information

Entry
Database: PDB / ID: 9l86
TitleStructure of frog TREX1
ComponentsThree-prime repair exonuclease 1
KeywordsIMMUNE SYSTEM / nuclease / DNase / innate immunity / autoimmunity / cancer
Biological speciesRanitomeya imitator (mimic poison frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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

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Assembly

Deposited unit
A: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4714
Polymers26,1831
Non-polymers2883
Water4,828268
1
A: Three-prime repair exonuclease 1
hetero molecules

A: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9428
Polymers52,3662
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area4590 Å2
ΔGint-98 kcal/mol
Surface area18280 Å2
MethodPISA
2
A: Three-prime repair exonuclease 1
hetero molecules

A: Three-prime repair exonuclease 1
hetero molecules

A: Three-prime repair exonuclease 1
hetero molecules

A: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,88516
Polymers104,7324
Non-polymers1,15312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area12170 Å2
ΔGint-210 kcal/mol
Surface area33580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.453, 86.090, 95.397
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-518-

HOH

21A-592-

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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.57 Å3/Da / Density % sol: 52.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.75 M (NH4)2SO4, 0.1 M Bis-Tris pH 5.5, 1.5% PEG3350

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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: Jan 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.4→35.18 Å / Num. obs: 51237 / % possible obs: 96.4 % / Redundancy: 11.1 % / Biso Wilson estimate: 13.08 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.022 / Net I/σ(I): 31.1
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3793 / CC1/2: 0.875 / Rpim(I) all: 0.192 / % possible all: 72.5

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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: 7TQN

7tqn


Resolution: 1.4→35.18 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1588 1995 3.89 %
Rwork0.1499 --
obs0.1502 51237 96.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.07 Å2
Refinement stepCycle: LAST / Resolution: 1.4→35.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1693 0 15 268 1976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091763
X-RAY DIFFRACTIONf_angle_d0.982407
X-RAY DIFFRACTIONf_dihedral_angle_d13.107647
X-RAY DIFFRACTIONf_chiral_restr0.079275
X-RAY DIFFRACTIONf_plane_restr0.008311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.27651010.24952474X-RAY DIFFRACTION69
1.44-1.480.2391280.20483153X-RAY DIFFRACTION88
1.48-1.520.21451420.18113491X-RAY DIFFRACTION97
1.52-1.570.1711470.1583612X-RAY DIFFRACTION99
1.57-1.620.17881430.16123547X-RAY DIFFRACTION99
1.62-1.690.15751460.15613607X-RAY DIFFRACTION99
1.69-1.770.1671450.15153597X-RAY DIFFRACTION99
1.77-1.860.16381470.15193628X-RAY DIFFRACTION100
1.86-1.980.15591470.13813616X-RAY DIFFRACTION100
1.98-2.130.14951470.1373645X-RAY DIFFRACTION100
2.13-2.340.15231480.1353652X-RAY DIFFRACTION100
2.34-2.680.13651490.13443677X-RAY DIFFRACTION100
2.68-3.380.15471490.14533699X-RAY DIFFRACTION100
3.38-35.180.15131560.1553844X-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)
12.25680.03910.11080.63490.01281.02050.0022-0.06520.06570.1342-0.02-0.0102-0.0815-0.03930.00970.0986-0.00480.00090.0616-0.02070.06530.614716.143613.6271
22.6305-1.0348-0.27723.95890.17120.4282-0.0986-0.28790.53330.22060.1168-0.1467-0.57960.1173-0.10450.2932-0.0774-0.01360.1531-0.0390.2344.060930.969812.2807
32.1678-0.19640.13830.9382-0.2211.42120.0640.01710.05280.0283-0.03270.1187-0.0474-0.1966-0.02720.07130.00980.00840.0849-0.020.0721.715713.572.8704
41.92620.55570.35461.85420.19460.70230.0258-0.14270.10490.1802-0.07690.1033-0.0524-0.08930.06580.1026-0.00870.00480.102-0.01060.061529.497713.883317.8211
51.09671.31170.11593.77380.06611.5931-0.0092-0.25380.42560.3293-0.04630.01-0.3617-0.10040.03590.29050.0587-0.02890.1309-0.09410.306430.888533.648820.368
60.10350.45140.222.91041.6370.9553-0.27180.02770.4416-0.1584-0.0410.2209-0.5906-0.11550.18560.22520.0077-0.04360.1025-0.00740.190830.067628.90479.4473
72.26311.6894-0.62174.70030.92920.92160.0888-0.2120.10850.2361-0.0985-0.032-0.21340.16650.02920.1544-0.0457-0.0310.1242-0.03230.101741.788522.913122.1213
81.4833-1.70140.34352.0697-0.73821.0882-0.0694-0.6281-0.29360.28250.10210.1818-0.0027-0.19880.02990.1391-0.01320.02960.14890.01420.080724.9948.528821.5781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 114 )
4X-RAY DIFFRACTION4chain 'A' and (resid 115 through 164 )
5X-RAY DIFFRACTION5chain 'A' and (resid 165 through 187 )
6X-RAY DIFFRACTION6chain 'A' and (resid 188 through 208 )
7X-RAY DIFFRACTION7chain 'A' and (resid 209 through 222 )
8X-RAY DIFFRACTION8chain 'A' and (resid 223 through 234 )

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