PDB-9l8a: Structure of frog TREX2

ID or keywords:

Entry

Database: PDB / ID: 9l8a

Title

Structure of frog TREX2

Components

exodeoxyribonuclease III

Keywords

IMMUNE SYSTEM / nuclease / DNase / innate immunity / autoimmunity / cancer

Function / homology

Function and homology information

exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / 3'-5'-DNA exonuclease activity / DNA catabolic process / DNA repair / DNA binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function

Biological species

Xenopus laevis (African clawed frog)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Zhu, J. / Wang, L. / Lin, C. / Zhou, W.

Funding support

China, 1items

Citation

Journal: 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

Deposition	Dec 27, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Apr 29, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9l8a.cif.gz	188.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9l8a.ent.gz	149.6 KB	Display	PDB format
PDBx/mmJSON format	9l8a.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l8/9l8a ftp://data.pdbj.org/pub/pdb/validation_reports/l8/9l8a	HTTPS FTP

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Related structure data

Related structure data	9l85C 9l86C 9l87C 9l88C 9l89C 9l8bC 9l8cC 9l8dC 7tqnS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

A: exodeoxyribonuclease III

B: exodeoxyribonuclease III

52.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	60.678, 62.355, 105.812
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	exodeoxyribonuclease III / Three-prime repair exonuclease 2 Mass: 26253.992 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC108706216 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8J1LJA4, exodeoxyribonuclease III
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.91 Å³/Da / Density % sol: 35.47 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 6.5, 5% PEG400

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 14, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.05→31.18 Å / Num. obs: 25220 / % possible obs: 97 % / Redundancy: 12.8 % / B_iso Wilson estimate: 23.77 Å² / CC_1/2: 0.992 / R_pim(I) all: 0.031 / Net I/σ(I): 27.2
Reflection shell	Resolution: 2.05→2.1 Å / Redundancy: 12.5 % / Mean I/σ(I) obs: 4 / Num. unique obs: 2044 / CC_1/2: 0.997 / R_pim(I) all: 0.222 / % possible all: 80.3

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Processing

Software

Name	Version	Classification
PHENIX	1.21.1_5127	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7TQN

7tqn

Resolution: 2.05→31.18 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.02 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2498	1983	7.86 %
R_work	0.2197	-	-
obs	0.2221	25220	97.04 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.05→31.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3370	0	0	319	3689

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	3446
X-RAY DIFFRACTION	f_angle_d	0.45	4656
X-RAY DIFFRACTION	f_dihedral_angle_d	11.255	1300
X-RAY DIFFRACTION	f_chiral_restr	0.038	524
X-RAY DIFFRACTION	f_plane_restr	0.003	602

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.05-2.1	0.3167	108	0.2994	1297	X-RAY DIFFRACTION	77
2.1-2.15	0.3319	134	0.2538	1520	X-RAY DIFFRACTION	91
2.15-2.22	0.2504	146	0.2387	1616	X-RAY DIFFRACTION	97
2.22-2.29	0.3001	138	0.2514	1664	X-RAY DIFFRACTION	98
2.29-2.37	0.2646	148	0.2374	1648	X-RAY DIFFRACTION	99
2.37-2.47	0.2571	137	0.2339	1684	X-RAY DIFFRACTION	99
2.47-2.58	0.2881	137	0.2407	1700	X-RAY DIFFRACTION	99
2.58-2.71	0.3047	150	0.2469	1690	X-RAY DIFFRACTION	100
2.71-2.88	0.2664	140	0.2397	1683	X-RAY DIFFRACTION	99
2.88-3.11	0.2621	152	0.2362	1700	X-RAY DIFFRACTION	100
3.11-3.42	0.2615	144	0.2132	1709	X-RAY DIFFRACTION	100
3.42-3.91	0.2028	148	0.1961	1739	X-RAY DIFFRACTION	100
3.91-4.93	0.2243	149	0.1735	1740	X-RAY DIFFRACTION	100
4.93-31.18	0.2125	152	0.2131	1847	X-RAY DIFFRACTION	100

Refinement TLS params.

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

ID	L11 (°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)
1	2.1748	-0.1995	-0.4587	1.8652	0.5375	3.6763	0.0798	-0.0164	-0.0112	0.0499	0.0541	0.0617	0.1849	-0.1493	-0.1347	0.0801	-0.0208	-0.0232	0.1045	0.0072	0.1732	9.6468	-6.3144	-8.0094
2	1.989	0.3368	-0.6147	2.6939	0.6685	2.6136	-0.1278	0.2464	-0.0808	-0.1152	0.1047	0.0845	0.3276	-0.275	-0.0004	0.1876	-0.0604	-0.0502	0.2304	0.0207	0.1107	4.9961	-15.5449	-14.3389
3	2.148	0.0378	0.7415	2.0061	0.3454	2.5733	0.0322	0.0801	0.3841	-0.0545	0.0661	-0.1801	-0.285	0.1234	-0.0501	0.1769	-0.0045	0.0199	0.0827	0.0034	0.2302	23.2303	7.8385	-11.024
4	4.9456	-1.5791	1.6107	4.6313	-0.2368	5.065	0.1551	-0.0471	0.5809	0.1075	-0.2126	-0.7856	0.4311	0.2291	0.0504	0.2109	0.0185	-0.0153	0.1431	-0.0194	0.2222	29.1742	-5.9417	0.6825
5	1.8658	0.0339	-0.4898	1.4429	-0.2605	0.2299	0.1993	0.5361	0.0918	-0.5811	0.2959	-0.1595	0.1933	0.6685	-0.16	0.4138	-0.0074	0.066	0.3831	-0.0471	0.1906	20.6082	2.5065	-27.9438
6	1.3327	0.431	1.9193	1.8592	0.1715	4.0159	-0.0993	-0.1923	0.4203	0.042	-0.127	0.5121	-0.1804	-0.7409	0.1394	0.1416	0.0088	0.0535	0.2323	0.0141	0.3321	10.5768	8.5375	-17.7089
7	2.1823	0.6804	1.227	1.1784	0.2877	2.6065	-0.2031	0.1595	0.1619	-0.079	0.0017	-0.1995	-0.2098	0.1437	0.1761	0.2259	-0.0182	0.0287	0.1577	0.0118	0.39	29.3305	11.8188	-11.4699
8	3.6323	0.1849	0.2979	2.9091	-0.9923	3.6181	0.0817	0.0476	-0.1982	0.0051	0.0764	-0.2598	0.3258	0.4402	-0.0926	0.1068	-0.0156	0.0438	0.1688	-0.0149	0.2435	32.3994	2.9841	-7.9828
9	2.9816	0.454	0.1275	2.7517	-0.2408	7.2733	-0.3823	-0.212	0.4372	-0.0043	0.4405	0.1194	-0.8662	-0.0395	0.0457	0.3755	0.0502	-0.1073	0.1374	0.0159	0.5156	23.7438	21.8718	-14.5701

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 103 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 104 through 223 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 3 through 39 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 40 through 54 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 55 through 84 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 85 through 103 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 104 through 176 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 177 through 211 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 212 through 223 )

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