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- PDB-9l8b: Structure of fish TREX2 -

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Basic information

Entry
Database: PDB / ID: 9l8b
TitleStructure of fish TREX2
Componentsexodeoxyribonuclease III
KeywordsIMMUNE SYSTEM / nuclease / DNase / innate immunity / autoimmunity / cancer
Function / homology
Function and homology information


exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / DNA catabolic process / nucleic acid binding / metal ion binding / cytoplasm
Similarity search - Function
Three-prime repair exonuclease 1/2 / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
exodeoxyribonuclease III
Similarity search - Component
Biological speciesCottoperca gobio (fish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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: exodeoxyribonuclease III
B: exodeoxyribonuclease III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3516
Polymers42,2542
Non-polymers974
Water3,081171
1
A: exodeoxyribonuclease III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1753
Polymers21,1271
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: exodeoxyribonuclease III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1753
Polymers21,1271
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.470, 78.510, 66.920
Angle α, β, γ (deg.)90.00, 103.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein exodeoxyribonuclease III


Mass: 21126.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cottoperca gobio (fish) / Gene: LOC115009440 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6J2PVC9, exodeoxyribonuclease III
#2: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.03 Å3/Da / Density % sol: 39.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1M MgCl2, 0.1 M Tris-HCl pH8.5, 35% PEG 4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.99→39.26 Å / Num. obs: 23028 / % possible obs: 99.29 % / Redundancy: 11.5 % / Biso Wilson estimate: 33.98 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.044 / Net I/σ(I): 10.5
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2818 / CC1/2: 0.368 / Rpim(I) all: 0.717 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5127refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→32.22 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2646 1152 5.01 %
Rwork0.2307 --
obs0.2324 23002 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.26 Å2
Refinement stepCycle: LAST / Resolution: 1.99→32.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2929 0 4 171 3104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022998
X-RAY DIFFRACTIONf_angle_d0.4774087
X-RAY DIFFRACTIONf_dihedral_angle_d11.561071
X-RAY DIFFRACTIONf_chiral_restr0.04476
X-RAY DIFFRACTIONf_plane_restr0.003532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.080.39791560.36972649X-RAY DIFFRACTION97
2.08-2.190.37671150.32132735X-RAY DIFFRACTION100
2.19-2.330.34161550.27772710X-RAY DIFFRACTION100
2.33-2.510.29711480.26132750X-RAY DIFFRACTION100
2.51-2.760.28991900.24612695X-RAY DIFFRACTION100
2.76-3.160.31171240.23362755X-RAY DIFFRACTION100
3.16-3.980.25791310.20972764X-RAY DIFFRACTION100
3.98-32.220.1871330.19072792X-RAY DIFFRACTION99
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)
14.5098-1.42320.43513.74970.18973.36980.16420.47420.1671-0.27190.1597-0.2012-0.3730.0826-0.22510.4398-0.05770.07820.3751-0.02440.37931.19922.5431.512
22.3519-0.67321.0232.1353-0.53062.1116-0.0753-0.06520.13960.16380.17650.2209-0.0658-0.3283-0.05290.374-0.01780.0550.34230.01980.3345-5.16317.14775.9116
31.50690.11210.41526.2071.28092.8153-0.06730.1925-0.1384-0.4320.2477-0.44-0.09870.2236-0.1840.3099-0.06160.0680.3241-0.02070.31558.7446-6.61853.1917
44.8729-1.58111.58146.60720.0785.14390.26840.20590.4687-0.6414-0.2953-0.4588-0.07170.4627-0.04820.39070.02120.10870.2949-0.02840.361611.23953.9506-29.5684
54.1481-1.08073.45924.6958-2.28834.2865-0.15340.0414-0.1928-0.00160.05080.15940.0621-0.00710.22540.3139-0.05510.11590.3272-0.07640.36372.95718.5773-29.3317
61.74380.28730.41666.0782.05431.75360.0076-0.13460.01550.1360.041-0.36110.13330.0837-0.06020.2688-0.01820.01490.28090.0480.313517.9312-1.4649-28.6521
73.9119-0.6629-0.49715.942.35342.32360.18740.0403-0.0906-0.0059-0.1541-0.0033-0.11350.0724-0.01030.4457-0.06820.0710.28850.04870.282112.8197-9.5621-29.7138
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 89 )
3X-RAY DIFFRACTION3chain 'A' and (resid 90 through 189 )
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 31 )
5X-RAY DIFFRACTION5chain 'B' and (resid 32 through 89 )
6X-RAY DIFFRACTION6chain 'B' and (resid 90 through 155 )
7X-RAY DIFFRACTION7chain 'B' and (resid 156 through 189 )

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