PDB-9l87: Structure of fish TREX1-DNA complex

ID or keywords:

Entry

Database: PDB / ID: 9l87

Title

Structure of fish 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')
exodeoxyribonuclease III

Keywords

IMMUNE SYSTEM/DNA / nuclease / DNase / innate immunity / autoimmunity / cancer / IMMUNE SYSTEM-DNA complex

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)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.99 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	9l87.cif.gz	198.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9l87.ent.gz	155.1 KB	Display	PDB format
PDBx/mmJSON format	9l87.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/l8/9l87 ftp://data.pdbj.org/pub/pdb/validation_reports/l8/9l87	HTTPS FTP

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Related structure data

Related structure data	9l85C 9l86C 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	#67 - Jul 2005 TATA-Binding Protein similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #253 - Jan 2021 Expressome similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (1)
#91 - Jul 2007
Thymine Dimers
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#135 - Mar 2011
Integrase
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#84 - Dec 2006
Transposase
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#3 - Mar 2000
DNA Polymerase
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#23 - Nov 2001
DNA
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#234 - Jun 2019
MDM2 and Cancer
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

B: exodeoxyribonuclease III

A: exodeoxyribonuclease III

F: 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

51.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: exodeoxyribonuclease III

F: 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

B: exodeoxyribonuclease III

defined by author&software
51.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	54.598, 135.960, 193.969
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

#1: Protein	exodeoxyribonuclease III / Three-prime repair exonuclease 1 Mass: 22387.467 Da / Num. of mol.: 2 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: DNA chain	DNA (5'-D(GPTPTPGPGPCPCPCPTPCPTPTPTPAPGPGPGPCPCPAPTPC)-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.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 3.5 Å³/Da / Density % sol: 60.23 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.3 M C6H5Na3O7, 20% 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: 0.97918 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: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.99→44.13 Å / Num. obs: 50061 / % possible obs: 99.54 % / Redundancy: 24.6 % / B_iso Wilson estimate: 37.61 Å² / CC_1/2: 0.999 / R_pim(I) all: 0.025 / Net I/σ(I): 12.1
Reflection shell	Resolution: 1.99→2.03 Å / Redundancy: 20.2 % / Mean I/σ(I) obs: 1.94 / Num. unique obs: 4896 / CC_1/2: 0.928 / R_pim(I) all: 0.342 / % possible all: 98.95

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Processing

Software

Name	Version	Classification
PHENIX	1.21.1_5127	refinement
DIALS		data scaling
DIALS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.99→41.71 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.97 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2137	2492	5.13 %
R_work	0.195	-	-
obs	0.196	49819	99.53 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.99→41.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3028	425	2	157	3612

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	3571
X-RAY DIFFRACTION	f_angle_d	1.145	4928
X-RAY DIFFRACTION	f_dihedral_angle_d	18.555	1348
X-RAY DIFFRACTION	f_chiral_restr	0.068	559
X-RAY DIFFRACTION	f_plane_restr	0.011	563

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 (%)
1.99-2.03	0.3157	155	0.3156	2593	X-RAY DIFFRACTION	99
2.03-2.07	0.2931	152	0.2893	2520	X-RAY DIFFRACTION	99
2.07-2.11	0.2617	128	0.2635	2610	X-RAY DIFFRACTION	99
2.11-2.16	0.2591	138	0.2444	2590	X-RAY DIFFRACTION	100
2.16-2.22	0.2804	143	0.2301	2586	X-RAY DIFFRACTION	99
2.22-2.28	0.2501	142	0.2352	2596	X-RAY DIFFRACTION	100
2.28-2.34	0.2536	138	0.2156	2584	X-RAY DIFFRACTION	99
2.35-2.42	0.2534	157	0.2243	2587	X-RAY DIFFRACTION	99
2.42-2.51	0.2413	150	0.2103	2582	X-RAY DIFFRACTION	99
2.51-2.61	0.2601	145	0.2105	2618	X-RAY DIFFRACTION	99
2.61-2.73	0.259	113	0.2135	2653	X-RAY DIFFRACTION	100
2.73-2.87	0.2417	129	0.2203	2624	X-RAY DIFFRACTION	99
2.87-3.05	0.283	135	0.2231	2648	X-RAY DIFFRACTION	100
3.05-3.28	0.2303	137	0.2126	2644	X-RAY DIFFRACTION	100
3.29-3.62	0.2164	158	0.1894	2628	X-RAY DIFFRACTION	100
3.62-4.14	0.192	155	0.1663	2665	X-RAY DIFFRACTION	100
4.14-5.21	0.1504	136	0.1519	2709	X-RAY DIFFRACTION	100
5.21-41.71	0.1857	144	0.1822	2827	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	2.5347	0.0442	0.6479	3.8331	-0.0313	2.9998	0.0401	0.014	0.1323	-0.0053	-0.0691	0.4044	0.1213	-0.1516	0.0184	0.3218	-0.0203	0.0458	0.2393	-0.0097	0.4941	-3.1942	-16.0296	-51.3123
2	3.8348	-0.2108	-0.8601	5.8725	0.3214	5.1358	0.0893	-0.0475	0.1568	0.123	-0.042	-0.625	0.1554	0.3625	-0.0714	0.3697	0.0054	-0.0274	0.2948	-0.0168	0.5156	12.7866	-15.8677	-46.3547
3	6.709	-0.2174	3.8673	4.3435	0.5911	5.0019	-0.2084	0.4719	0.8748	-0.6323	0.0953	0.1106	-0.3068	0.0764	0.3131	0.4221	0.0081	0.0055	0.2566	0.0197	0.5791	-3.6718	-5.9263	-53.9633
4	6.8869	-0.3226	3.3335	3.5947	0.5915	8.359	-0.4235	0.003	0.5768	0.4129	-0.0778	0.6625	-0.1786	-0.6182	0.2796	0.3265	-0.0396	0.0221	0.2399	-0.0403	0.5949	-11.5029	-18.3294	-50.0721
5	5.3216	2.1602	2.9787	6.0138	0.9004	5.691	0.0022	-0.1928	0.5267	0.1367	-0.1087	0.9445	-0.3933	-0.314	0.1226	0.3797	0.0125	0.1218	0.2675	-0.0498	0.613	-8.2903	-8.0602	-44.4176
6	6.4947	-3.966	2.2561	2.6683	-0.7056	3.2377	0.2903	-0.3334	-0.6991	0.5955	-0.2478	1.7089	0.8646	-0.3462	-0.0055	0.3372	-0.0674	0.1236	0.3242	-0.0847	0.5784	-14.5177	-28.344	-47.9001
7	4.6399	3.0947	-0.4019	5.5115	-0.6855	0.8318	-0.2979	0.3318	-0.3783	-0.5664	0.1004	-0.2189	0.2794	0.0029	0.2307	0.4565	-0.0291	0.0791	0.2886	-0.076	0.462	-5.1751	-31.1447	-54.7705
8	1.6297	2.8421	1.6788	5.4619	2.6688	2.101	-0.0101	0.3168	0.4171	0.1165	-0.2274	2.5898	-1.2055	-0.621	0.4585	0.618	0.0679	0.0278	0.4955	-0.1267	1.1835	-20.5976	-22.6261	-50.4752
9	0.7322	-0.0511	-0.7322	0.8484	-1.9688	5.3719	0.5118	0.191	-0.3311	-0.033	-0.2792	-0.0546	-0.1003	0.6354	-0.3139	0.6627	-0.0002	-0.0532	0.5275	0.0191	0.5076	7.0827	-18.6116	-80.6336
10	2.8898	-0.098	2.7978	1.4163	0.8937	7.6937	0.0796	0.389	-0.1086	-0.4361	0.1157	0.0526	-0.3572	0.1118	-0.2143	0.5416	0.0051	0.0329	0.3499	0.0132	0.3686	4.816	-16.5376	-80.1922
11	2.0121	-0.9399	-3.0113	1.9689	0.4913	4.915	-0.038	0.0493	-0.1254	-0.7354	-0.4468	0.3939	0.2156	-0.8437	0.5873	0.9766	0.067	-0.0029	0.8509	0.0689	0.8629	0.4624	-7.6569	-66.2824
12	1.1531	0.5846	2.1846	7.8252	2.9242	5.3088	0.0704	0.9485	0.0973	-0.678	0.3064	-1.0365	-0.8935	1.2817	-0.4451	0.6826	-0.1516	0.1374	0.7194	-0.0461	0.4709	17.4894	-11.3592	-74.434
13	0.9411	0.3113	-0.0488	0.8692	-0.0866	0.581	0.003	0.0522	-2.1264	-1.3455	0.3953	0.2494	0.526	-0.3924	-0.4712	1.3886	0.3606	-0.5874	1.2753	-0.081	1.1837	11.8277	-32.6621	-72.003
14	3.6716	3.605	-4.3714	7.5553	-1.8871	7.0247	0.0133	0.1227	0.6753	0.0222	-0.1604	1.3816	-1.0242	-0.1872	0.075	0.6257	0.0075	-0.1211	0.3716	-0.0366	0.7937	25.0596	-35.2636	-57.0344
15	1.7374	-2.4262	1.796	2.8969	-3.133	1.9416	0.4553	0.266	-1.6017	-0.15	-0.1674	0.8374	0.3675	0.2783	-0.3204	0.8191	0.1339	-0.2183	0.6578	0.0738	1.0559	15.8655	-34.3609	-64.8848

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 24 through 60 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 61 through 95 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 96 through 109 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 110 through 123 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 124 through 147 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 148 through 158 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 159 through 197 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 198 through 211 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 25 through 44 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 45 through 174 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 175 through 184 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 185 through 211 )
13	X-RAY DIFFRACTION	13	chain 'F' and (resid 2 through 6 )
14	X-RAY DIFFRACTION	14	chain 'F' and (resid 7 through 11 )
15	X-RAY DIFFRACTION	15	chain 'F' and (resid 12 through 22 )

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