PDB-9ava: Co-crystal structure of human TREX1 in complex with an inhibitor

ID or keywords:

Entry

Database: PDB / ID: 9ava

Title

Co-crystal structure of human TREX1 in complex with an inhibitor

Components

Three-prime repair exonuclease 1

Keywords

TRANSPORT PROTEIN / TREX1 / SGC

Function / homology

Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Phage conserved hypothetical protein BR0599 / : / : / Bacteriophage phiJL001 Gp84 C-terminal domain-containing protein

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Dehghani-Tafti, S. / Dong, A. / Li, Y. / Xu, J. / Ackloo, S. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)

Funding support

1items

Citation

Journal: To be published
Title: Co-crystal structure of human TREX1 in complex with an inhibitor
Authors: Dehghani-Tafti, S. / Dong, A. / Li, Y. / Xu, J. / Ackloo, S. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)

History

Deposition	Mar 1, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 15, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ava.cif.gz	982.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9ava.ent.gz		Display	PDB format
PDBx/mmJSON format	9ava.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9ava_validation.pdf.gz	4.9 MB	Display	wwPDB validaton report
Full document	9ava_full_validation.pdf.gz	4.9 MB	Display
Data in XML	9ava_validation.xml.gz	90.5 KB	Display
Data in CIF	9ava_validation.cif.gz	125.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/av/9ava ftp://data.pdbj.org/pub/pdb/validation_reports/av/9ava	HTTPS FTP

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Related structure data

Related structure data	8vl7C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Three-prime repair exonuclease 1

B: Three-prime repair exonuclease 1

C: Three-prime repair exonuclease 1

D: Three-prime repair exonuclease 1

E: Three-prime repair exonuclease 1

F: Three-prime repair exonuclease 1

G: Three-prime repair exonuclease 1

H: Three-prime repair exonuclease 1

I: Three-prime repair exonuclease 1

J: Three-prime repair exonuclease 1

K: Three-prime repair exonuclease 1

L: Three-prime repair exonuclease 1

hetero molecules

305 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Three-prime repair exonuclease 1

D: Three-prime repair exonuclease 1

hetero molecules

defined by author&software
50.8 kDa, 2 polymers

2

B: Three-prime repair exonuclease 1

F: Three-prime repair exonuclease 1

hetero molecules

defined by author&software
50.8 kDa, 2 polymers

3

C: Three-prime repair exonuclease 1

E: Three-prime repair exonuclease 1

hetero molecules

defined by author&software
50.8 kDa, 2 polymers

4

G: Three-prime repair exonuclease 1

H: Three-prime repair exonuclease 1

hetero molecules

defined by author&software
50.8 kDa, 2 polymers

5

I: Three-prime repair exonuclease 1

J: Three-prime repair exonuclease 1

hetero molecules

defined by author&software
50.8 kDa, 2 polymers

6

K: Three-prime repair exonuclease 1

L: Three-prime repair exonuclease 1

hetero molecules

defined by author&software
50.8 kDa, 2 polymers

Unit cell

Length a, b, c (Å)	136.120, 288.960, 178.840
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Three-prime repair exonuclease 1 / 3'-5' exonuclease TREX1 / Deoxyribonuclease III / DNase III Mass: 24817.555 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TREX1 / Cell (production host): BL21(DE3)V2R-pRARE2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NSU2, exodeoxyribonuclease III
#2: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: K
#3: Chemical	ChemComp-A1AG1 / (2R)-2-[(5R,6S,8R,9aS)-8-amino-1-oxo-5-(2-phenylethyl)hexahydro-1H-pyrrolo[1,2-a][1,4]diazepin-2(3H)-yl]-N-[(3,4-dichlorophenyl)methyl]-4-methylpentanamide Mass: 545.544 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₂₉H₃₈Cl₂N₄O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	... ChemComp-UNX / UNKNOWN ATOM OR ION Num. of mol.: 29 / Source method: obtained synthetically
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 669 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.95 Å³/Da / Density % sol: 58.34 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 200mM KBr, 8% PEG 20K, 8% PEG 550 MME, 100mM Tris [pH 7.5]

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.97911 Å

Detector

Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 24, 2021

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97911 Å / Relative weight: 1

Reflection

Resolution: 2.3→50 Å / Num. obs: 151765 / % possible obs: 98.2 % / Redundancy: 4 % / CC_1/2: 0.982 / CC star: 0.995 / R_merge(I) obs: 0.167 / R_pim(I) all: 0.094 / R_rim(I) all: 0.193 / Χ²: 1.525 / Net I/σ(I): 7.6 / Num. measured all: 602739

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.3-2.34	3.5	0.983	7523	0.401	0.757	0.593	1.156	1.754	98
2.34-2.38	4	0.948	7577	0.425	0.772	0.541	1.098	1.766	99.2
2.38-2.43	4	0.834	7599	0.473	0.801	0.476	0.966	1.704	99.6
2.43-2.48	4.1	0.781	7640	0.503	0.818	0.442	0.903	1.747	99.6
2.48-2.53	4	0.725	7630	0.558	0.846	0.413	0.84	1.728	99.5
2.53-2.59	4	0.64	7628	0.599	0.866	0.366	0.742	1.711	99.4
2.59-2.66	4	0.559	7622	0.672	0.897	0.32	0.648	1.703	99.2
2.66-2.73	4	0.457	7561	0.759	0.929	0.26	0.529	1.692	99
2.73-2.81	4	0.404	7632	0.797	0.942	0.232	0.47	1.704	99
2.81-2.9	3.9	0.328	7626	0.866	0.963	0.188	0.381	1.694	98.9
2.9-3	3.9	0.267	7531	0.906	0.975	0.154	0.31	1.676	97.9
3-3.12	3.8	0.206	7520	0.944	0.986	0.118	0.239	1.622	97.8
3.12-3.26	3.6	0.159	7331	0.968	0.992	0.095	0.187	1.599	95.2
3.26-3.44	3.7	0.137	7590	0.97	0.992	0.081	0.16	1.532	98.5
3.44-3.65	4.2	0.108	7722	0.986	0.996	0.059	0.124	1.444	99.6
3.65-3.93	4.2	0.083	7693	0.992	0.998	0.045	0.095	1.352	99.5
3.93-4.33	4.2	0.065	7694	0.995	0.999	0.035	0.074	1.173	99
4.33-4.95	4.1	0.059	7616	0.996	0.999	0.031	0.067	1.093	97.7
4.95-6.24	3.9	0.06	7424	0.996	0.999	0.033	0.069	1.118	94.5
6.24-50	4.2	0.039	7606	0.999	1	0.02	0.044	0.831	94

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Processing

Software

Name	Version	Classification
BUSTER	2.10.3	refinement
HKL-3000		data scaling
HKL-3000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→35 Å / Cor.coef. F_o:F_c: 0.93 / Cor.coef. F_o:F_c free: 0.905 / SU R Cruickshank DPI: 0.252 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.246 / SU R_free Blow DPI: 0.199 / SU R_free Cruickshank DPI: 0.203

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.239	7535	5.03 %	RANDOM
R_work	0.202	-	-	-
obs	0.204	149711	96.5 %	-

Displacement parameters

B_iso mean: 33.73 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.2464 Å²	0 Å²	0 Å²
2-	-	3.1012 Å²	0 Å²
3-	-	-	-0.8548 Å²

Refine analyze

Luzzati coordinate error obs: 0.3 Å

Refinement step

Cycle: 1 / Resolution: 2.3→35 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18783	0	484	669	19936

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	19910	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.07	27280	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		6399	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes
X-RAY DIFFRACTION	t_gen_planes		3429	HARMONIC	5
X-RAY DIFFRACTION	t_it		19910	HARMONIC	20
X-RAY DIFFRACTION	t_nbd		8	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_omega_torsion	3.34
X-RAY DIFFRACTION	t_other_torsion	17.03
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		2606	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		23355	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.3→2.32 Å / Total num. of bins used: 50

	R_factor	Num. reflection	% reflection
R_free	0.3606	144	4.81 %
R_work	0.2647	2851	-
all	0.2689	2995	-
obs	-	-	77.67 %

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	1.2421	-0.0596	0.3639	1.1584	-0.6954	2.1493	-0.0242	0.1801	-0.0148	-0.0113	-0.0591	-0.146	0.1133	0.416	0.0833	-0.1466	0.0141	0.0293	0.1501	-0.0134	-0.1158	-68.0276	-28.7023	-26.4568
2	0.925	-0.0916	-0.1282	1.0972	-0.8537	2.1754	0.0236	-0.0933	-0.0558	0.087	-0.1189	-0.1673	-0.1219	0.2909	0.0954	-0.1429	-0.0188	-0.0105	0.0958	0.0062	-0.0854	-0.1312	-44.353	-19.9353
3	2.5248	-0.2144	0.0452	1.1587	0.6439	2.5157	0.0165	-0.2827	0.1049	0.1667	0.1564	-0.2154	0.0159	0.3423	-0.1729	-0.1564	0.0198	-0.0201	0.0745	-0.0608	-0.1214	-46.4825	-37.3752	12.1433
4	1.114	-0.11	0.2406	1.1086	-0.536	2.3956	-0.0108	-0.0587	-0.116	-0.0313	0.1296	0.1909	0.157	-0.2746	-0.1188	-0.1301	-0.0126	0.0264	0.0703	0.0419	-0.0813	-91.946	-34.6988	-15.973
5	3.5626	0.2459	0.5115	1.1801	0.4225	3.1703	-0.005	-0.7548	0.2117	0.1917	-0.0395	0.0846	0.0997	-0.3697	0.0445	-0.1819	0.0409	0.0343	0.2022	-0.0579	-0.2593	-69.9497	-33.6873	23.4917
6	1.436	0.2183	-0.0521	1.0618	-0.6383	1.9755	0.0559	0.1168	0.0514	0.0558	0.0546	0.1198	-0.1185	-0.3122	-0.1105	-0.1334	0.0175	0.017	0.0617	0.0229	-0.0716	-23.3418	-38.2671	-31.4467
7	1.5484	0.6959	0.0781	2.9166	-0.017	0.6249	0.0563	-0.065	-0.1652	0.1484	-0.0186	-0.4379	0.0203	0.1043	-0.0377	-0.1366	0.0245	-0.0176	0.0913	0.0221	-0.0855	-23.1124	-78.9343	-4.3478
8	1.1179	0.4302	-0.1562	2.6582	-0.0239	0.5678	0.0185	0.0199	0.1161	0.103	0.0013	0.3406	0.0056	-0.0493	-0.0198	-0.0926	0.0157	0.0153	0.101	0.0049	-0.0423	-46.5862	-66.8346	-6.41
9	1.7707	0.0544	0.1287	2.8929	-0.0173	0.7401	0.0817	-0.0421	0.038	0.2525	-0.1557	-0.3892	-0.1461	0.1011	0.074	-0.0838	-0.0258	-0.0247	0.044	0.0712	-0.1183	-22.2083	-6.4494	-46.0658
10	2.5062	1.1193	-0.2963	2.8575	-0.0471	1.1529	0.2283	-0.1292	0.5241	0.4018	-0.177	0.5564	-0.2482	-0.1708	-0.0514	-0.0705	0.0515	0.1205	-0.0313	-0.0406	-0.1012	-45.8271	5.51	-43.0543
11	2.1481	0.165	0.5583	1.7307	0.955	1.977	-0.0126	-0.1889	0.1598	0.0136	-0.2203	0.2856	-0.2186	-0.4296	0.2329	-0.1501	0.04	-0.0039	0.0872	-0.0555	-0.1254	-0.9598	-39.6216	14.5239
12	1.5701	-0.0166	-0.1875	2.619	1.3819	2.8791	0.0197	-0.1291	0.1374	0.0197	-0.0249	-0.1741	-0.3553	0.059	0.0052	-0.0944	-0.0571	-0.0284	-0.0182	-0.0204	-0.1323	22.3241	-30.5691	22.7388

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|* }
2	X-RAY DIFFRACTION	2	{ B\|* }
3	X-RAY DIFFRACTION	3	{ C\|* }
4	X-RAY DIFFRACTION	4	{ D\|* }
5	X-RAY DIFFRACTION	5	{ E\|* }
6	X-RAY DIFFRACTION	6	{ F\|* }
7	X-RAY DIFFRACTION	7	{ G\|* }
8	X-RAY DIFFRACTION	8	{ H\|* }
9	X-RAY DIFFRACTION	9	{ I\|* }
10	X-RAY DIFFRACTION	10	{ J\|* }
11	X-RAY DIFFRACTION	11	{ K\|* }
12	X-RAY DIFFRACTION	12	{ L\|* }

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