PDB-3mxj: Crystal Structure of the mTREX1 Apoprotein

ID or keywords:

Entry

Database: PDB / ID: 3mxj

Title

Crystal Structure of the mTREX1 Apoprotein

Components

Three prime repair exonuclease 1

Keywords

HYDROLASE / RNase H-like fold / Polyproline II helix

Function / homology

Function and homology information

immune response in brain or nervous system / adenyl deoxyribonucleotide binding / CD86 biosynthetic process / immune complex formation / cellular response to type I interferon / organ or tissue specific immune response / atrial cardiac muscle tissue development / activation of immune response / DNA synthesis involved in UV-damage excision repair / T cell antigen processing and presentation ...immune response in brain or nervous system / adenyl deoxyribonucleotide binding / CD86 biosynthetic process / immune complex formation / cellular response to type I interferon / organ or tissue specific immune response / atrial cardiac muscle tissue development / activation of immune response / DNA synthesis involved in UV-damage excision repair / T cell antigen processing and presentation / MutSalpha complex binding / retrotransposition / oligosaccharyltransferase complex / regulation of lysosome organization / regulation of fatty acid metabolic process / regulation of lipid biosynthetic process / DNA modification / WW domain binding / heart process / MutLalpha complex binding / regulation of protein complex stability / cellular response to hydroxyurea / lymphoid progenitor cell differentiation / regulation of type I interferon production / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / macrophage activation involved in immune response / regulation of tumor necrosis factor production / regulation of cellular respiration / inflammatory response to antigenic stimulus / DNA catabolic process / regulation of immunoglobulin production / apoptotic cell clearance / regulation of T cell activation / regulation of glycolytic process / DNA duplex unwinding / DNA binding, bending / 3'-5'-DNA exonuclease activity / negative regulation of type I interferon-mediated signaling pathway / DNA metabolic process / : / negative regulation of cGAS/STING signaling pathway / type I interferon-mediated signaling pathway / regulation of innate immune response / blood vessel development / nuclear replication fork / cellular response to interferon-beta / heart morphogenesis / response to UV / mitotic G1 DNA damage checkpoint signaling / negative regulation of innate immune response / 3'-5' exonuclease activity / DNA damage checkpoint signaling / generation of precursor metabolites and energy / kidney development / determination of adult lifespan / protein-DNA complex / establishment of protein localization / cellular response to gamma radiation / cellular response to reactive oxygen species / cellular response to UV / single-stranded DNA binding / cellular response to oxidative stress / regulation of inflammatory response / regulation of gene expression / double-stranded DNA binding / defense response to virus / adaptive immune response / DNA replication / protein stabilization / inflammatory response / immune response / innate immune response / DNA damage response / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / DNA binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Bailey, S.L. / Hollis, T.

Citation

Journal: To be Published
Title: X-ray Crystal Structures of TREX1 3' Exonuclease Autoimmune Disease Mutants
Authors: Bailey, S.L. / Harvey, S. / Perrino, F.W. / Hollis, T.

History

Deposition	May 7, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 18, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Feb 21, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3mxj.cif.gz	181 KB	Display	PDBx/mmCIF format
PDB format	pdb3mxj.ent.gz	145.8 KB	Display	PDB format
PDBx/mmJSON format	3mxj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3mxj_validation.pdf.gz	432.5 KB	Display	wwPDB validaton report
Full document	3mxj_full_validation.pdf.gz	437.8 KB	Display
Data in XML	3mxj_validation.xml.gz	19.4 KB	Display
Data in CIF	3mxj_validation.cif.gz	27.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mx/3mxj ftp://data.pdbj.org/pub/pdb/validation_reports/mx/3mxj	HTTPS FTP

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Related structure data

Related structure data	3mxiC 3mxmC 2ioc 2oa8 3mxk PDB Unreleased entry C: citing same article (ref.)
Similar structure data	2ioc-d 5vdt-1 6nao-2 4o67-2 3usk-4 2nrf-d 5vdw-2 4lkv-1 5vdo-1 2o4g-2 Search similar-shape structures by Omokage search (details) 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

Deposited unit

B: Three prime repair exonuclease 1

A: Three prime repair exonuclease 1

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	64.160, 85.720, 100.270
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Three prime repair exonuclease 1 / 3'-5' exonuclease TREX1 Mass: 26323.961 Da / Num. of mol.: 2 / Fragment: N-terminal fragment, residues 1-242 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trex1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q91XB0, exodeoxyribonuclease III
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Three prime repair exonuclease 1 / 3'-5' exonuclease TREX1

Mass: 26323.961 Da / Num. of mol.: 2 / Fragment: N-terminal fragment, residues 1-242
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Gene: Trex1 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q91XB0, exodeoxyribonuclease III

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.62 Å³/Da / Density % sol: 53.03 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.25 M tri-sodium citrate dihydrate 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
Detector	Type: RIGAKU / Detector: IMAGE PLATE
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 1.95→29 Å / Num. obs: 40918 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.72 % / B_iso Wilson estimate: 24.71 Å² / R_merge(I) obs: 0.057 / Net I/σ(I): 16
Reflection shell	Resolution: 1.95→2.02 Å / Redundancy: 4.63 % / R_merge(I) obs: 0.276 / Mean I/σ(I) obs: 4.1 / % possible all: 97.1

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Processing

Software

Name	Version	Classification
CrystalClear		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.4_113)	refinement
d*TREK		data reduction
d*TREK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.95→28.781 Å / SU ML: 0.27 / σ(F): 1.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2371	2044	5.03 %	Random
R_work	0.2038	-	-	-
obs	0.2055	40666	99.21 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 35.365 Å² / k_sol: 0.351 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	6.1263 Å²	-0 Å²	-0 Å²
2-	-	-0.8299 Å²	0 Å²
3-	-	-	-5.2964 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→28.781 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3311	0	0	242	3553

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3393
X-RAY DIFFRACTION	f_angle_d	1.05	4623
X-RAY DIFFRACTION	f_dihedral_angle_d	15.608	1260
X-RAY DIFFRACTION	f_chiral_restr	0.068	528
X-RAY DIFFRACTION	f_plane_restr	0.005	601

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 (%)
1.95-2.0197	0.272	186	0.2106	3702	X-RAY DIFFRACTION	97
2.0197-2.1005	0.2759	209	0.1963	3820	X-RAY DIFFRACTION	100
2.1005-2.1961	0.2369	220	0.1962	3841	X-RAY DIFFRACTION	100
2.1961-2.3118	0.3541	181	0.3145	3720	X-RAY DIFFRACTION	96
2.3118-2.4566	0.2489	187	0.2051	3884	X-RAY DIFFRACTION	100
2.4566-2.6462	0.2541	195	0.198	3872	X-RAY DIFFRACTION	100
2.6462-2.9122	0.2627	192	0.2202	3908	X-RAY DIFFRACTION	100
2.9122-3.3331	0.2668	212	0.2101	3900	X-RAY DIFFRACTION	100
3.3331-4.1973	0.1922	213	0.1755	3913	X-RAY DIFFRACTION	100
4.1973-28.7838	0.1917	249	0.1723	4062	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	3.03	1.0377	-1.8722	1.188	-0.8284	1.9411	0.2308	0.204	0.135	0.1121	-0.0827	0.1223	-0.3239	-0.1767	-0.162	0.1364	0.0028	0.0399	0.1004	-0.0054	0.1258	-6.3099	5.0236	36.2964
2	0.4977	-0.7228	0.41	0.7979	-0.2827	1.4199	-0.0495	0.251	0.2238	0.0358	-0.0267	-0.0646	-0.0298	0.1536	0.0714	0.1079	-0.0095	-0.0101	0.1141	-0.0035	0.1523	8.6111	3.1549	30.7256
3	0.0691	0.2871	-0.4337	5.2762	-2.4076	2.1064	0.2538	-0.5505	-0.2152	-0.1897	0.3506	0.952	0.1727	-0.4377	-0.4674	0.1621	-0.1564	-0.0646	0.3423	0.0636	0.2975	-12.5892	-8.7544	32.0146
4	1.1962	0.6495	0.2233	0.799	-0.7334	1.6774	0.0001	0.2317	-0.0182	0.0226	0.0222	-0.149	0.1176	0.1422	-0.003	0.0892	0.0125	0.0055	0.1183	-0.0239	0.1349	3.466	0.454	23.2287
5	2.3526	1.7606	2.1361	1.4917	1.2271	3.0742	0.5478	0.0437	-0.4872	-0.0171	0.0155	-0.5859	0.533	0.0224	-0.4667	0.4173	0.114	-0.0635	0.3378	0.0447	0.4208	19.9476	-5.8269	28.3604
6	3.9826	-1.8241	1.0447	0.9274	-0.309	0.5726	0.0718	0.6843	-0.2596	-0.1305	-0.1848	0.2148	0.0976	0.2774	0.0949	0.2002	-0.0221	-0.0189	0.339	0.0137	0.1979	17.9627	3.8799	17.76
7	0.2987	-0.0789	-0.3532	0.2107	-0.2503	1.2829	0.0611	0.0106	0.0195	0.194	-0.0698	-0.0157	-0.2671	-0.0599	0.016	0.1654	-0.0172	-0.0195	0.1441	0.0042	0.1685	-0.074	9.6525	28.2866
8	0.3058	0.8344	-0.4266	2.9408	-1.9136	1.7895	0.1113	0.0447	-0.0517	0.2006	-0.0134	-0.0004	-0.1649	0.3031	-0.0753	0.1075	-0.0413	-0.0084	0.1561	-0.0092	0.1577	9.1076	11.9161	33.2942
9	1.2534	0.1137	0.2068	2.4344	0.6523	0.2801	-0.0144	-0.1822	0.1636	0.4175	0.0625	0.0773	0.0125	-0.0006	-0.0084	0.161	-0.0154	0.0009	0.1701	-0.0078	0.1453	-1.282	2.2571	40.709
10	0.2978	-0.078	0.3432	0.841	-0.7049	0.6605	0.0454	0.0131	-0.0767	0.0266	-0.0572	-0.1769	0.0426	0.0281	0.0148	0.1996	-0.0149	-0.0102	0.1392	0.013	0.1756	1.0837	-15.2791	38.6684
11	2.6223	0.6709	-2.605	0.2592	-0.5526	2.9483	-0.2608	-0.0841	-0.4219	-0.1432	-0.0511	-0.0838	0.3773	0.0899	0.2335	0.1728	-0.0083	-0.0118	0.1384	0.0206	0.1913	-0.3098	-7.7879	30.7085
12	0.0372	-0.0867	-0.0205	0.3894	-0.0566	1.313	-0.0144	-0.0474	-0.0712	0.1234	0.0858	-0.0276	-0.0595	-0.4507	-0.0504	0.1743	0.0103	0.051	0.2664	0.008	0.2074	-9.6225	-1.282	42.5109
13	3.8972	1.4654	-1.2722	2.2766	0.1463	1.3551	-0.0434	-0.6627	0.0571	0.501	0.0447	-0.0246	-0.1574	0.354	-0.033	0.211	-0.0224	-0.0321	0.2163	-0.0375	0.2015	7.454	11.753	40.2546
14	2.7311	-0.0071	-1.8678	1.7751	0.1021	1.6729	-0.094	0.2182	-0.1341	-0.3703	0.1303	-0.1509	0.1066	0.0171	-0.0488	0.2094	-0.0444	0.0643	0.219	-0.0052	0.1571	7.502	3.4981	0.3743
15	1.6286	-1.1506	0.7439	0.9523	-0.4022	1.2104	0.1721	-0.0865	0.1277	-0.1893	-0.0858	-0.0015	0.1228	-0.1875	-0.0661	0.1445	-0.018	-0.0444	0.1917	-0.0026	0.158	-10.2888	2.3156	8.3683
16	0.5729	-0.3466	-0.5609	3.1462	-3.3186	5.1241	-0.1629	-0.5519	0.1328	-0.1179	-0.0891	-1.2459	0.3324	0.5769	0.2476	0.1629	0.0586	0.0415	0.3349	0.0087	0.2957	15.6939	-3.4131	6.6624
17	1.7077	-0.3041	-2.5384	0.2143	0.7704	4.8014	-0.6099	0.2108	-0.2022	0.8522	-0.1611	-0.7973	0.6501	-0.1032	0.6858	0.4238	0.0672	-0.1017	0.1375	0.0406	0.6682	9.2726	-18.1067	8.1817
18	0.0978	-0.495	0.244	1.7715	-0.3173	2.0982	0.136	-0.2285	-0.4453	-0.1361	0.0676	0.4475	0.2588	-0.5563	-0.186	0.1427	-0.0653	-0.0559	0.2438	0.0496	0.2315	-9.9788	-1.0043	14.7265
19	0.1724	0.6752	0.3733	4.8771	-2.027	6.89	0.0963	-0.2097	-0.0358	0.0726	0.0616	0.6222	0.2478	-1.2118	-0.1715	0.1208	0.0476	-0.0232	0.4179	0.0165	0.2096	-17.1414	6.1027	20.535
20	1.2308	-0.2262	-0.5725	0.0537	0.3043	1.3874	0.0403	0.027	0.0833	-0.0968	-0.0281	-0.0288	-0.3022	0.0483	-0.0105	0.1441	-0.0016	-0.0053	0.1159	0.0084	0.1303	2.3396	10.5948	11.3064
21	0.3754	-0.3355	0.274	1.919	0.598	0.7859	0.0131	0.0751	-0.0453	-0.2944	-0.1049	0.2106	-0.073	-0.2088	0.0916	0.1705	-0.0207	-0.033	0.2185	-0.0153	0.1692	-8.6019	3.5658	1.4237
22	8.8326	-5.8861	-4.1844	4.0453	3.1875	3.8782	0.403	-0.0482	0.6302	-0.3657	-0.1293	-0.4023	-0.6539	-0.2234	-0.1772	0.2101	0.039	-0.0445	0.1217	0.0108	0.1349	-6.9244	16.9236	7.7435
23	1.0827	0.728	-0.1961	0.3244	-0.048	0.0272	0.049	0.263	-0.0426	-0.0787	-0.016	0.0477	0.0183	-0.01	-0.014	0.2148	-0.0135	0.0174	0.2277	-0.0583	0.1866	1.1861	-4.4678	-3.6103
24	0.9152	0.2142	-1.1001	0.8306	-1.3961	3.3861	-0.3061	-0.0121	0.1085	-0.2318	0.0883	-0.5482	0.8243	0.0433	0.0936	0.3677	-0.0661	-0.0146	0.137	-0.0599	0.2973	-2.751	-16.3862	5.2361
25	1.3172	-0.3128	-0.6853	0.7187	0.6185	2.565	-0.1538	0.1017	-0.1861	-0.1634	-0.01	-0.1694	0.3122	0.0214	0.1611	0.1765	0.0045	0.0312	0.1678	-0.0137	0.1844	4.5947	-5.6359	2.386
26	2.4474	-0.6505	1.1987	1.0545	-0.1544	0.6813	-0.019	0.2173	0.1542	-0.2898	0.0502	0.1391	-0.2113	-0.2624	-0.0262	0.1851	0.027	-0.0269	0.244	0.0431	0.1501	-8.4483	10.4672	-1.8213

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 6:19)
2	X-RAY DIFFRACTION	2	(chain A and resid 20:41)
3	X-RAY DIFFRACTION	3	(chain A and resid 42:58)
4	X-RAY DIFFRACTION	4	(chain A and resid 59:77)
5	X-RAY DIFFRACTION	5	(chain A and resid 78:86)
6	X-RAY DIFFRACTION	6	(chain A and resid 87:99)
7	X-RAY DIFFRACTION	7	(chain A and resid 100:127)
8	X-RAY DIFFRACTION	8	(chain A and resid 128:146)
9	X-RAY DIFFRACTION	9	(chain A and resid 147:162)
10	X-RAY DIFFRACTION	10	(chain A and resid 163:192)
11	X-RAY DIFFRACTION	11	(chain A and resid 194:210)
12	X-RAY DIFFRACTION	12	(chain A and resid 211:223)
13	X-RAY DIFFRACTION	13	(chain A and resid 224:234)
14	X-RAY DIFFRACTION	14	(chain B and resid 4:19)
15	X-RAY DIFFRACTION	15	(chain B and resid 20:40)
16	X-RAY DIFFRACTION	16	(chain B and resid 41:46)
17	X-RAY DIFFRACTION	17	(chain B and resid 47:59)
18	X-RAY DIFFRACTION	18	(chain B and resid 60:88)
19	X-RAY DIFFRACTION	19	(chain B and resid 89:100)
20	X-RAY DIFFRACTION	20	(chain B and resid 101:122)
21	X-RAY DIFFRACTION	21	(chain B and resid 123:137)
22	X-RAY DIFFRACTION	22	(chain B and resid 138:147)
23	X-RAY DIFFRACTION	23	(chain B and resid 148:176)
24	X-RAY DIFFRACTION	24	(chain B and resid 177:195)
25	X-RAY DIFFRACTION	25	(chain B and resid 196:224)
26	X-RAY DIFFRACTION	26	(chain B and resid 225:234)

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