PDB-9l85: Structure of fish TREX1

ID or keywords:

Entry

Database: PDB / ID: 9l85

Title

Structure of fish TREX1

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 / DNA catabolic process / nucleic acid binding / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Labeo rohita (rohu)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.91 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	9l85.cif.gz	315.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9l85.ent.gz	259.8 KB	Display	PDB format
PDBx/mmJSON format	9l85.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/l8/9l85 ftp://data.pdbj.org/pub/pdb/validation_reports/l8/9l85	HTTPS FTP

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Related structure data

Related structure data	9l86C 9l87C 9l88C 9l89C 9l8aC 9l8bC 9l8cC 9l8dC 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

C: exodeoxyribonuclease III

D: exodeoxyribonuclease III

89.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: exodeoxyribonuclease III

defined by author
Evidence: light scattering, gel filtration
22.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: exodeoxyribonuclease III

defined by author
22.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: exodeoxyribonuclease III

defined by author
22.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: exodeoxyribonuclease III

defined by author
22.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	74.680, 86.860, 132.850
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 Mass: 22387.467 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Labeo rohita (rohu) / Gene: ROHU_009745 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A498LXZ6, exodeoxyribonuclease III
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.41 Å³/Da / Density % sol: 48.87 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.3 M KSCN, 15% PEG 3350

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9792 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 24, 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: 2.91→32.55 Å / Num. obs: 19553 / % possible obs: 99.9 % / Redundancy: 12.8 % / B_iso Wilson estimate: 65.93 Å² / CC_1/2: 0.997 / R_pim(I) all: 0.086 / Net I/σ(I): 8.7
Reflection shell	Resolution: 2.91→3.06 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2723 / CC_1/2: 0.589 / R_pim(I) all: 0.622 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.21.1_5127	refinement
xia2		data scaling
xia2		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.91→30.35 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.91 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2693	3638	9.98 %
R_work	0.2336	-	-
obs	0.2372	19536	99.61 %

Solvent computation

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

Displacement parameters

B_iso mean: 68.62 Å²

Refinement step

Cycle: LAST / Resolution: 2.91→30.35 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6091	0	0	1	6092

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	6231
X-RAY DIFFRACTION	f_angle_d	0.533	8452
X-RAY DIFFRACTION	f_dihedral_angle_d	15.783	2297
X-RAY DIFFRACTION	f_chiral_restr	0.039	954
X-RAY DIFFRACTION	f_plane_restr	0.005	1095

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 (%)
2.91-2.95	0.3681	133	0.3837	1254	X-RAY DIFFRACTION	99
2.95-2.99	0.3621	149	0.3719	1297	X-RAY DIFFRACTION	99
2.99-3.03	0.3584	135	0.3734	1221	X-RAY DIFFRACTION	100
3.03-3.08	0.4213	139	0.3511	1284	X-RAY DIFFRACTION	100
3.08-3.12	0.3761	137	0.3264	1272	X-RAY DIFFRACTION	100
3.12-3.18	0.3869	140	0.3337	1255	X-RAY DIFFRACTION	100
3.18-3.23	0.3615	141	0.3169	1240	X-RAY DIFFRACTION	99
3.23-3.29	0.3346	137	0.3193	1266	X-RAY DIFFRACTION	99
3.29-3.35	0.33	137	0.2983	1286	X-RAY DIFFRACTION	100
3.35-3.42	0.3448	134	0.288	1239	X-RAY DIFFRACTION	100
3.42-3.49	0.3166	142	0.278	1263	X-RAY DIFFRACTION	100
3.49-3.58	0.3348	145	0.2574	1304	X-RAY DIFFRACTION	100
3.58-3.67	0.2614	137	0.2399	1236	X-RAY DIFFRACTION	100
3.67-3.76	0.2983	141	0.2334	1275	X-RAY DIFFRACTION	99
3.76-3.87	0.2268	144	0.2163	1237	X-RAY DIFFRACTION	100
3.87-4	0.2743	138	0.2127	1272	X-RAY DIFFRACTION	100
4-4.14	0.2627	142	0.2065	1274	X-RAY DIFFRACTION	100
4.14-4.31	0.2679	138	0.1961	1256	X-RAY DIFFRACTION	100
4.31-4.5	0.2074	144	0.1756	1268	X-RAY DIFFRACTION	100
4.5-4.74	0.2393	145	0.1879	1271	X-RAY DIFFRACTION	100
4.74-5.04	0.179	141	0.1754	1243	X-RAY DIFFRACTION	100
5.04-5.42	0.2331	141	0.218	1282	X-RAY DIFFRACTION	100
5.42-5.96	0.2861	139	0.2292	1237	X-RAY DIFFRACTION	100
5.96-6.82	0.2568	138	0.2506	1286	X-RAY DIFFRACTION	100
6.82-8.56	0.2357	141	0.1899	1257	X-RAY DIFFRACTION	100
8.56-30.35	0.1971	140	0.1822	1245	X-RAY DIFFRACTION	98

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	0.4574	0.5783	-0.4987	0.8299	-0.7471	0.617	-0.0811	-0.2409	-0.0148	-0.0566	0.0547	0.1074	-0.1043	0.0536	-0	0.5948	0.014	0.0397	0.4035	-0.0615	0.4785	32.5473	6.4425	8.1313
2	0.1194	0.2646	-0.2817	1.1362	-0.4343	0.6635	0.0768	0.4218	-0.7779	-0.1171	0.0621	-0.251	-0.1818	-0.5238	-0.0003	0.8975	0.0923	0.0573	0.7561	-0.1429	0.8794	33.873	-9.9096	10.7658
3	1.8127	0.1959	0.5555	0.6819	-0.7104	1.0333	0.0183	0.29	-0.3874	-0.1508	-0.0932	0.3906	0.1659	-0.3504	0.0005	0.4538	0.0155	0.0443	0.36	0.0104	0.4341	37.8346	9.4046	6.1137
4	1.6738	0.1503	-0.4527	0.6946	0.2207	0.582	0.171	1.292	-0.607	-0.6326	-0.495	0.2175	0.0894	-0.2753	-0.0179	0.7441	-0.0691	0.2397	0.602	0.0206	0.6614	43.3091	13.5678	1.9442
5	2.0428	-0.4488	-1.6696	1.1426	-0.6765	2.3113	0.0889	0.4863	-0.2833	-0.1451	0.1761	0.0473	0.2577	-0.4669	0.0007	0.446	-0.0302	-0.0799	0.4251	0.0019	0.4125	22.3867	12.0927	18.3343
6	5.033	0.6714	-0.3334	4.5898	-1.2392	4.0726	0.1619	-0.2242	-0.9241	-0.6758	-0.1493	-0.6981	-0.0682	0.5436	1.3175	0.2227	-0.0992	0.0062	0.0915	0.0293	0.4623	31.8677	24.3323	13.4401
7	2.7705	0.5968	-0.6207	1.7576	-1.5467	1.8686	0.23	-0.1619	0.1554	-0.1872	-0.1774	-0.4286	-0.1264	-0.2292	0.0211	0.2489	0.0259	-0.0947	0.5903	0.032	0.3667	2.5865	-14.6889	11.3648
8	1.5148	1.3844	1.1957	2.3157	0.1467	1.7188	0.4089	0.2962	0.4968	-0.1194	-0.032	-0.3578	-0.081	0.1773	0.0066	0.5586	0.1182	0.0487	0.7538	0.1604	0.5248	4.3283	-2.2926	9.0421
9	0.7274	0.0321	-0.7777	0.2648	-0.1073	0.8316	0.243	0.2863	0.3307	-0.2233	-0.068	0.085	-0.4059	0.3329	0.0001	0.6395	0.0882	0.0154	0.7858	0.0855	0.7611	3.4401	-6.6298	0.9289
10	0.6012	-0.1583	-0.3714	0.0225	0.1024	0.2256	0.198	0.1142	0.06	0.156	0.3497	-0.3308	-0.2754	-0.3255	-0.001	0.6123	-0.0018	-0.0031	0.6152	-0.1734	0.6154	4.1662	-21.376	11.4183
11	0.0088	-0.0421	0.0447	0.6171	0.0621	0.3365	0.2803	-0.2498	0.5803	0.1432	-0.0686	-0.0219	0.7041	-0.147	0.0111	0.4195	0.0749	0.0992	0.621	0.0646	0.4729	-6.25	-13.4696	9.5512
12	0.0987	-0.1242	0.0035	0.2082	-0.0723	0.0822	-0.2619	1.4335	0.6207	-0.9806	0.3971	0.3193	0.6827	-0.452	-0.0022	0.8014	-0.2736	-0.0769	0.9789	0.0157	0.7778	-5.4437	-20.9446	2.3922
13	0.0943	0.1699	0.2336	1.5273	1.454	1.4323	-0.2052	0.2792	-0.1809	0.5732	0.2824	-0.1064	0.5455	-0.2515	0.0593	0.3373	0.0145	0.017	0.4577	-0.0068	0.3635	13.581	-21.1867	23.3102
14	1.1293	-0.5195	-0.2028	0.2941	-0.2394	1.9735	0.1079	0.3049	0.7353	0.0502	0.356	-0.8103	-0.9654	0.6318	0.0056	0.757	-0.0736	0.1228	1.0438	0.0812	0.884	16.6709	-14.8353	14.2382
15	1.4062	-0.4202	-0.4544	0.2399	-0.0438	0.4524	0.2977	-0.4133	-0.9126	0.1301	-0.1302	0.6992	0.3541	0.2134	-0.0391	0.3084	0.0196	-0.0279	0.3971	-0.0314	0.7093	5.7217	-30.5194	14.7738
16	1.4134	-0.9937	-0.401	0.6515	0.2624	0.0965	0.1396	0.1466	-0.426	-0.0394	-0.0151	0.0906	-0.0974	0.0924	-0.0002	0.4286	0.0017	0.054	0.4192	0.035	0.4694	25.358	13.2464	45.0673
17	1.0068	0.2122	-1.0758	0.6363	-0.2594	1.1145	0.2475	-0.2813	0.0371	-0.2491	-0.3862	0.175	0.0651	-0.0353	-0.0068	0.5232	0.0556	0.0104	0.4376	0.0044	0.5573	8.71	8.7694	43.1868
18	0.7121	-1.0797	-0.9141	1.5486	1.3581	1.1424	-0.1908	-0.2667	-0.4026	0.098	0.2042	0.3048	0.2439	0.4319	0.0186	0.4725	-0.0213	0.0001	0.4801	-0.0278	0.4081	27.9539	17.2935	47.7755
19	0.5087	0.2064	0.1815	0.0806	0.0723	0.0607	-0.0817	0.1053	-0.1284	0.4626	0.3378	0.0532	-0.7409	-0.5649	-0.0001	0.5686	0.0127	-0.0278	0.4723	0.1102	0.4863	21.6274	23.4816	42.203
20	1.986	-0.8655	0.2165	3.3096	-4.0231	5.7375	-0.0966	-0.0417	0.2892	1.0365	0.3749	-0.6719	-1.31	-0.0514	3.9019	0.6904	-0.1856	0.0335	0.5804	-0.2469	0.4698	26.679	25.9909	50.0527
21	0.0165	0.0777	0.0787	0.2225	0.2373	0.224	-0.3237	-0.0195	0.053	-0.2638	0.2287	-0.1002	-0.1154	0.1667	0.0001	0.4575	-0.0087	0.0457	0.426	0.0255	0.5271	35.4183	7.8306	29.9257
22	0.2697	-0.0065	-0.1973	1.3508	0.7873	1.892	-0.236	-0.1284	0.1157	-0.212	-0.1729	0.247	-0.7412	-0.1603	-0.1006	0.4881	0.0835	0.0451	0.5562	0.1278	0.5873	30.8648	2.5628	39.3611
23	2.061	2.0116	0.85	6.6477	1.5956	0.679	0.0438	0.182	-0.3821	0.4228	0.2636	-0.9465	-0.1223	0.3032	0.4584	0.336	-0.006	0.0004	0.3968	0.0441	0.2783	41.3823	18.509	38.2973
24	2.6473	-0.5812	2.2392	3.3579	-0.4881	2.1925	-0.5527	-0.6317	0.7342	-0.1197	0.4213	-0.0046	0.6994	0.3411	-0.0448	0.396	0.0139	0.0134	0.2089	-0.03	0.3426	10.8904	-21.4251	42.9849
25	0.62	0.4851	-0.6251	0.744	-0.5458	0.631	-0.6334	0.247	1.0129	0.4139	0.4705	-0.6812	0.2713	-0.7388	-0.0097	0.5122	0.0303	-0.1205	0.626	-0.0142	0.4692	13.5423	-14.591	49.377
26	1.6981	1.0285	1.4022	1.7706	0.2535	1.4505	-0.1195	0.0352	0.0221	-0.2748	0.0693	-0.3036	0.5566	0.4889	-0.0204	0.3715	0.0469	-0.0463	0.461	0.0995	0.4107	28.6898	-14.4367	43.8138
27	1.5205	0.8981	0.2645	0.5936	-0.1352	0.8903	-0.0217	-0.0437	-0.0501	0.0666	0.0791	-0.0393	0.1394	-0.0873	-0.0001	0.3757	0.0834	0.0093	0.4019	0.0368	0.3924	11.3789	-24.557	47.169
28	0.2106	-0.6192	-0.2727	1.8773	0.8157	0.3545	-1.0974	0.1062	-2.3167	1.0826	1.3814	0.4238	0.3834	-0.4275	-0.0612	0.7238	-0.1727	-0.0061	0.7502	0.1153	0.7741	9.0864	-31.1674	51.1811
29	0.1539	-0.0415	0.0236	0.6878	-0.2249	0.0645	-0.3652	0.359	-0.202	-0.0728	0.0207	0.0112	-0.2408	0.0914	-0.0088	0.3981	-0.0113	-0.0149	0.3437	-0.0269	0.4408	1.9567	-13.6001	30.3014
30	1.042	2.7109	-0.7064	9.6156	-1.8944	0.4859	1.3857	0.4907	0.2339	0.0215	-0.2342	2.5232	0.4391	0.9377	1.4629	0.8021	0.0755	-0.16	1.0171	0.0167	1.0729	11.0689	-3.2918	36.1139
31	2.322	-0.0403	2.1326	0.353	-1.3048	6.5983	-0.3024	-0.4238	0.2167	0.0791	-0.0532	0.0687	-0.255	-1.8206	0.5578	0.491	0.1361	-0.017	0.551	-0.1532	0.5226	4.3193	-10.0044	41.4277
32	1.0938	1.4719	-1.5808	2.356	-1.3523	3.8508	-0.1163	-0.0743	0.4095	0.2568	0.2632	0.2352	0.4329	-1.0293	0.2781	0.4429	-0.1233	-0.0411	0.3199	-0.0391	0.3685	-3.9924	-24.078	39.0765

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 24 through 60 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 61 through 95 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 96 through 135 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 136 through 147 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 148 through 197 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 198 through 211 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 24 through 44 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 45 through 86 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 87 through 109 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 110 through 123 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 124 through 135 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 136 through 147 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 148 through 174 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 175 through 197 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 198 through 211 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 23 through 60 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 61 through 95 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 96 through 123 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 124 through 134 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 135 through 147 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 148 through 173 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 174 through 197 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 198 through 211 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 23 through 44 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 45 through 60 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 61 through 95 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 96 through 135 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 136 through 147 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 148 through 173 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 174 through 182 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 183 through 197 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 198 through 211 )

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