PDB-6ea6: Structure of VACV poxin 2'3' cGAMP-specific nuclease

ID or keywords:

Entry

Database: PDB / ID: 6ea6

Title

Structure of VACV poxin 2'3' cGAMP-specific nuclease

Components

Protein B2

Keywords

HYDROLASE / Vaccina virus / nuclease / cGAS / cGAMP / poxvirus / innate immunity

Function / homology

Nucleopolyhedrovirus p26 protein / Poxin, virus / 2',3'-cyclic GMP-AMP binding / nuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / Poxin

Function and homology information

Biological species

Vaccinia virus WR

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.703 Å

Authors

Eaglesham, J.B. / Kranzusch, P.J.

Citation

Journal: Nature / Year: 2019
Title: Viral and metazoan poxins are cGAMP-specific nucleases that restrict cGAS-STING signalling.
Authors: Eaglesham, J.B. / Pan, Y. / Kupper, T.S. / Kranzusch, P.J.

History

Deposition	Aug 2, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 6, 2019	Provider: repository / Type: Initial release
Revision 1.1	Feb 20, 2019	Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Feb 27, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Dec 11, 2019	Group: Derived calculations Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list Item: _pdbx_struct_assembly_prop.value
Revision 1.4	Oct 23, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6ea6.cif.gz	337.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6ea6_validation.pdf.gz	441.8 KB	Display	wwPDB validaton report
Full document	6ea6_full_validation.pdf.gz	446.3 KB	Display
Data in XML	6ea6_validation.xml.gz	36.6 KB	Display
Data in CIF	6ea6_validation.cif.gz	53.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ea/6ea6 ftp://data.pdbj.org/pub/pdb/validation_reports/ea/6ea6	HTTPS FTP

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Related structure data

Related structure data	6ea8C 6ea9C C: citing same article (ref.)
Similar structure data	1lvh-d 5e52-d 2dbt-d 1u5e-d 1pu8-d 1t6l-1 2io4-2 5jvt-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

A: Protein B2

C: Protein B2

B: Protein B2

D: Protein B2

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

1

A: Protein B2

B: Protein B2

defined by author&software
Evidence: gel filtration
50.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Protein B2

D: Protein B2

defined by author&software
50.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	55.026, 93.194, 94.133
Angle α, β, γ (deg.)	90.00, 105.63, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Protein B2 Mass: 25071.490 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus WR / Strain: Western Reserve / Gene: VACWR184, B2R / Production host: Escherichia coli (E. coli) / References: UniProt: Q01225
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 750 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.35 Å³/Da / Density % sol: 47.63 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 100 mM HEPES-NaOH pH 7.0, 20-22% PEG-2000 MME

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Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 14, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.7→46.6 Å / Num. obs: 99918 / % possible obs: 99.3 % / Redundancy: 38.6 % / CC_1/2: 0.93 / R_pim(I) all: 0.049 / Net I/σ(I): 20.3
Reflection shell	Resolution: 1.7→1.73 Å / Redundancy: 22.6 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4418 / CC_1/2: 0.558 / R_pim(I) all: 0.642 / % possible all: 89.6

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.703→46.597 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1822	1994	2.13 %	5
R_work	0.1599	-	-	-
obs	0.1603	93415	93.49 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.703→46.597 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6160	0	0	750	6910

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	6320
X-RAY DIFFRACTION	f_angle_d	1.102	8562
X-RAY DIFFRACTION	f_dihedral_angle_d	11.832	3710
X-RAY DIFFRACTION	f_chiral_restr	0.084	909
X-RAY DIFFRACTION	f_plane_restr	0.007	1093

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 (%)
1.7031-1.7457	0.2609	86	0.2466	4007	X-RAY DIFFRACTION	57
1.7457-1.7929	0.2728	154	0.221	6626	X-RAY DIFFRACTION	96
1.7929-1.8457	0.2041	148	0.2014	6959	X-RAY DIFFRACTION	100
1.8457-1.9052	0.2369	122	0.1905	6029	X-RAY DIFFRACTION	86
1.9052-1.9733	0.1891	136	0.1678	5749	X-RAY DIFFRACTION	83
1.9733-2.0524	0.2108	140	0.158	6115	X-RAY DIFFRACTION	88
2.0524-2.1458	0.1973	149	0.1574	6962	X-RAY DIFFRACTION	100
2.1458-2.2589	0.2086	149	0.1589	6969	X-RAY DIFFRACTION	100
2.2589-2.4004	0.1647	157	0.165	6965	X-RAY DIFFRACTION	100
2.4004-2.5857	0.1775	150	0.1744	6967	X-RAY DIFFRACTION	100
2.5857-2.8459	0.1959	150	0.1672	6959	X-RAY DIFFRACTION	100
2.8459-3.2576	0.2086	150	0.1632	7000	X-RAY DIFFRACTION	100
3.2576-4.1039	0.1357	150	0.1396	7004	X-RAY DIFFRACTION	100
4.1039-46.6143	0.1655	153	0.1437	7110	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	1.2694	-0.1146	0.4261	2.1524	-0.0539	2.0776	0.1162	0.1712	-0.0436	-0.1514	0.0472	-0.4638	0.0767	0.5725	-0.1756	0.1696	0.0307	0.0326	0.2689	-0.0555	0.2491	8.1673	7.0183	-1.7771
2	2.9358	0.9974	1.6032	3.1717	1.5331	3.0077	0.1597	-0.3897	0.0518	0.3751	-0.1116	0.0163	0.0379	-0.0887	-0.0416	0.2092	-0.0326	0.0094	0.1994	-0.0117	0.1262	-1.7811	12.2401	13.9837
3	2.6042	0.2678	-0.0909	3.5888	0.7248	4.7887	-0.0406	0.194	-0.0105	-0.3617	-0.0322	-0.1407	-0.0518	0.296	0.0078	0.1798	0.0121	0.0079	0.1725	-0.0133	0.1594	-4.7597	9.2792	-5.3502
4	2.1567	0.1575	-0.1601	2.9283	-0.1304	2.2918	0.1698	-0.1873	0.2507	0.0997	-0.1048	-0.216	-0.2778	0.1258	-0.0991	0.2344	-0.0197	0.0168	0.1924	-0.0241	0.2059	-0.7241	20.1052	8.1296
5	3.4895	-0.648	0.759	2.9353	1.0111	3.7717	0.0397	-0.0996	0.0945	0.1981	-0.0845	-0.1	0.0869	0.2481	-0.0489	0.1483	-0.0316	0.0085	0.1697	-0.036	0.1528	2.6803	14.0964	8.677
6	1.4	0.0739	0.7922	2.1606	0.3388	1.613	0.0884	0.1288	0.0505	-0.2891	-0.0703	0.0652	-0.0387	0.0156	-0.014	0.2003	0.024	0.0112	0.1704	-0.0096	0.158	-8.1606	8.977	-5.0576
7	3.4448	0.9829	0.1269	3.7986	-1.3768	1.2687	0.2042	-0.1747	0.1023	-0.0555	-0.2457	0.402	-0.2031	-0.8388	-0.0654	0.225	0.126	-0.0701	0.3435	-0.0582	0.2639	-26.1616	13.6928	-7.5376
8	1.9375	1.7069	1.7538	6.644	4.9045	7.0888	0.0687	0.9344	0.1145	-0.4541	-0.7134	1.6683	0.1561	-1.1509	0.0568	0.3736	0.0848	-0.1422	0.6483	-0.0449	0.7104	-33.3116	8.6142	-13.674
9	1.4445	0.8649	1.0875	0.9516	0.0825	2.2896	0.0824	0.4174	-0.0301	-0.3878	-0.1144	0.2933	-0.0694	-0.3232	0.0659	0.2879	0.0852	-0.1051	0.3126	-0.077	0.2382	-18.3012	6.4983	-14.9992
10	1.36	-0.0314	1.6565	0.951	0.37	2.9311	0.1643	0.1134	-0.0031	-0.3131	-0.1045	0.333	-0.1504	-0.1824	-0.0799	0.211	0.0497	-0.0589	0.2169	-0.0489	0.2237	-18.1023	7.2842	-6.8635
11	2.646	0.9527	1.3713	3.5861	0.4169	3.2746	0.3077	-0.5021	0.4222	0.3996	-0.1429	0.5661	0.2174	-0.7125	-0.2018	0.2078	-0.0736	0.06	0.3428	-0.0064	0.3646	-22.6684	-14.6058	-43.246
12	3.8076	-0.4146	1.9843	4.0303	-1.6096	3.3073	0.0226	0.6512	0.2143	-0.4094	-0.0588	0.3678	-0.0088	0.0403	0.0248	0.2718	0.0528	-0.0368	0.2886	0.0245	0.1951	-13.7576	-10.5792	-60.1045
13	2.9091	0.5717	0.542	3.8107	-1.0029	5.0775	0.1194	-0.1815	0.155	0.2453	-0.107	0.1478	-0.192	-0.3061	0.0078	0.1294	0.0057	0.0183	0.1447	-0.0167	0.165	-10.1176	-12.484	-40.5796
14	2.6492	-0.0779	0.1347	4.8611	-0.2596	2.9179	0.1447	0.1849	0.5562	-0.2944	-0.1145	0.5676	-0.3368	-0.1333	0.0373	0.2485	0.0456	-0.0007	0.216	0.0198	0.3387	-14.4155	-2.2527	-54.6447
15	4.0895	1.4828	0.2564	3.8229	-0.3293	3.2156	0.0165	0.3547	0.1724	-0.3991	-0.0461	0.5191	0.1084	-0.3092	0.0104	0.1797	0.0599	-0.0491	0.226	0.0344	0.2759	-17.8997	-8.1346	-54.7113
16	1.1849	-0.0478	1.162	1.8899	-0.1728	2.0274	0.05	-0.1032	0.0479	0.0887	-0.0789	0.1098	0.1715	-0.0813	-0.028	0.1379	0.0129	0.0402	0.1826	-0.0027	0.1593	-9.5069	-14.8123	-42.5053
17	3.3975	-0.1631	0.6218	3.1163	-0.3744	2.5227	0.0125	0.1592	0.3569	0.0445	-0.0708	-0.2537	-0.2687	0.2955	0.0259	0.1649	-0.0512	0.0156	0.1722	0.0182	0.1726	7.2598	-8.2833	-38.5936
18	3.457	-0.1844	0.0471	6.5073	-2.3207	5.7112	-0.2389	-0.2397	-0.0997	0.5351	-0.2988	-1.657	-0.1834	1.2371	-0.1116	0.2039	-0.0317	-0.0127	0.4658	-0.0296	0.5534	18.5782	-13.4996	-33.168
19	1.558	-0.3468	0.3288	1.3192	-0.1167	2.647	-0.0194	-0.1744	0.0689	0.1848	-0.1045	-0.1715	0.0424	0.1499	0.0272	0.1678	-0.0254	-0.0036	0.1728	0.0028	0.1478	3.4265	-14.8167	-30.4164
20	1.416	-0.5008	1.2983	1.0766	-0.2852	2.5577	0.0752	0.0416	0.0716	0.0439	-0.0525	-0.0456	-0.0837	0.0967	-0.0207	0.1535	-0.0129	0.0178	0.1663	0.0068	0.1744	3.0868	-14.4672	-39.4368
21	3.6708	-0.8365	-1.4605	3.195	0.7294	2.5708	0.2952	0.6528	-0.417	-0.2668	-0.243	0.479	-0.1663	-0.6409	-0.0461	0.3106	0.0891	-0.0523	0.4465	-0.0506	0.5548	-35.6335	-7.6117	-2.3128
22	3.7394	0.2639	-1.21	3.4637	-0.4554	3.5838	-0.0753	-0.8967	-0.3286	0.4434	0.013	0.4393	0.1001	-0.2958	-0.0409	0.2978	-0.0734	0.0804	0.41	0.002	0.3318	-26.7721	-11.2008	14.6482
23	3.7467	-0.4695	1.185	3.5875	-0.7373	7.264	0.0443	0.1588	-0.1367	-0.2015	-0.1857	0.3677	0.2769	-0.4953	0.0424	0.1775	-0.0251	-0.0044	0.2465	-0.0857	0.2798	-23.1162	-9.5418	-4.8022
24	5.2447	-0.4136	0.1879	3.6629	-0.6549	2.6517	0.1341	-0.5292	-0.4268	0.3873	0.002	0.4304	0.1256	-0.3809	-0.0255	0.2826	-0.0591	0.028	0.3276	0.0334	0.3967	-29.3851	-16.2412	9.3287
25	2.5616	-0.2069	-0.7607	2.5292	-0.3589	2.2968	0.146	0.1088	-0.0881	-0.0664	-0.2004	0.3439	-0.0153	-0.0157	-0.0675	0.1893	0.0049	-0.0407	0.2332	-0.0591	0.2911	-22.4559	-7.3217	-3.0032
26	3.6346	-0.328	-0.6238	2.3892	0.2197	3.5332	0.017	0.1501	-0.1732	-0.0515	-0.0565	-0.165	-0.0002	0.2379	0.0668	0.1822	0.0177	-0.0201	0.1703	-0.0428	0.1642	-3.2979	-10.5984	-10.649
27	1.1943	-0.0154	-1.1015	1.053	0.3684	2.8713	0.1036	0.0532	-0.0802	-0.0952	-0.0577	0.0919	0.1003	-0.0406	-0.0378	0.2009	0.0085	-0.0042	0.1915	-0.0286	0.1776	-9.738	-7.6811	-5.9382
28	2.2867	0.2161	-0.4146	3.069	-0.2828	2.6711	0.1838	-0.0733	-0.138	0.178	-0.0828	-0.8237	-0.1721	0.6508	-0.1201	0.1724	-0.0421	-0.018	0.2697	-0.0134	0.4217	20.4038	-29.1943	-43.2225
29	3.2613	-0.8137	-0.6185	3.1843	0.7882	2.6461	0.2023	0.7287	-0.0055	-0.6202	-0.1378	-0.3575	-0.0545	0.1235	-0.0303	0.3006	0.0598	0.0746	0.2997	-0.032	0.2292	11.2869	-34.1113	-59.6853
30	3.4324	-0.291	1.4696	3.2038	0.8378	6.5626	-0.098	-0.1578	-0.1216	0.1421	0.0598	-0.2797	-0.0183	0.316	-0.0204	0.1334	0.0162	-0.0064	0.1587	0.0054	0.1894	7.9639	-31.4492	-40.4308
31	3.3313	-0.1533	0.3364	2.6603	0.9898	2.6684	0.2013	0.3824	-0.1304	-0.4319	-0.086	-0.4785	0.091	0.2675	-0.1176	0.2201	0.0602	0.0722	0.2314	-0.043	0.2866	14.1122	-38.6854	-54.1149
32	1.6513	-0.2691	-0.2394	2.0679	0.1766	1.877	0.0095	-0.0526	-0.0137	-0.0473	-0.0746	-0.1924	-0.041	-0.0115	0.0141	0.1227	0.0033	0.0026	0.1508	-0.0008	0.1801	7.3638	-29.241	-42.305
33	4.3917	-0.654	-1.2166	2.3767	-0.1029	1.6484	0.055	0.1617	-0.2696	0.0842	-0.12	0.2177	0.1005	-0.302	0.0337	0.1476	-0.0304	-0.0053	0.1642	-0.0098	0.1889	-9.4207	-35.8789	-37.7232
34	4.4582	1.6983	1.7059	6.4755	5.3015	6.5127	-0.2153	-0.6603	0.4145	0.2895	-0.9158	2.1982	-0.2132	-1.0667	0.0949	0.279	-0.008	0.0346	0.3937	-0.0483	0.6404	-20.7279	-30.9289	-32.2384
35	1.9269	0.7678	0.594	3.0185	0.9528	1.6846	0.0936	-0.308	-0.0034	0.5104	-0.2272	0.2107	0.0554	-0.0995	0.0691	0.1832	-0.0377	0.0214	0.1547	-0.0062	0.1433	-5.6072	-28.5279	-30.1558
36	1.0926	0.1951	-1.2962	1.4	0.5145	3.2708	0.1272	0.0036	-0.1018	0.1411	-0.0948	0.0957	0.0828	-0.1346	-0.0564	0.161	-0.0026	-0.0086	0.1708	-0.0011	0.1589	-5.3532	-29.5487	-39.0777

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 29 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 30 through 49 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 50 through 66 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 67 through 79 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 80 through 98 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 99 through 124 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 125 through 137 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 138 through 150 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 151 through 164 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 165 through 194 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 2 through 29 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 30 through 49 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 50 through 66 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 67 through 79 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 80 through 98 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 99 through 117 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 118 through 137 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 138 through 150 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 151 through 163 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 164 through 194 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 2 through 29 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 30 through 49 )
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 50 through 66 )
24	X-RAY DIFFRACTION	24	chain 'B' and (resid 67 through 98 )
25	X-RAY DIFFRACTION	25	chain 'B' and (resid 99 through 117 )
26	X-RAY DIFFRACTION	26	chain 'B' and (resid 118 through 163 )
27	X-RAY DIFFRACTION	27	chain 'B' and (resid 164 through 194 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 2 through 29 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 30 through 49 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 50 through 66 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 67 through 98 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 99 through 117 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 118 through 137 )
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 138 through 150 )
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 151 through 163 )
36	X-RAY DIFFRACTION	36	chain 'D' and (resid 164 through 194 )

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