PDB-6ea9: Structure of VACV Poxin in post-reactive state with Gp[2'-5']Ap[3']

ID or keywords:

Entry

Database: PDB / ID: 6ea9

Title

Structure of VACV Poxin in post-reactive state with Gp[2'-5']Ap[3']

Components

Protein B2

Keywords

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

Function / homology

Nucleopolyhedrovirus p26 protein / Poxin, virus / symbiont-mediated suppression of host innate immune response / nuclease activity / 2',3'-cyclic GMP-AMP binding / host cell cytoplasm / Hydrolases; Acting on ester bonds / 2',5'-GpAp / Poxin

Function and homology information

Biological species

Vaccinia virus WR

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.1 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	Jan 29, 2020	Group: Derived calculations / Category: pdbx_struct_assembly_prop / pdbx_struct_oper_list Item: _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.name ..._pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[3]
Revision 1.4	Mar 13, 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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PDBx/mmCIF format	6ea9.cif.gz	411.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6ea9_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	6ea9_full_validation.pdf.gz	2.1 MB	Display
Data in XML	6ea9_validation.xml.gz	41.3 KB	Display
Data in CIF	6ea9_validation.cif.gz	52.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ea/6ea9 ftp://data.pdbj.org/pub/pdb/validation_reports/ea/6ea9	HTTPS FTP

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Related structure data

Related structure data	6ea6C 6ea8C C: citing same article (ref.)
Similar structure data	6ea8-1 5ma6-d 5ma8-2 5ma8-1 5mu6-2 5uut-1 2qt3-1 5mad-2 4me6-d 4fhx-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

B: Protein B2

C: Protein B2

D: Protein B2

E: Protein B2

hetero molecules

127 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Protein B2

B: Protein B2

hetero molecules

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

2

C: Protein B2

D: Protein B2

hetero molecules

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

3

E: Protein B2

hetero molecules

E: Protein B2

hetero molecules

defined by author&software
50.9 kDa, 2 polymers

Unit cell

Length a, b, c (Å)	215.416, 57.147, 133.113
Angle α, β, γ (deg.)	90.00, 120.37, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Protein B2 Mass: 24743.227 Da / Num. of mol.: 5 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: Chemical	ChemComp-9BG / 2',5'-GpAp / [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methyl [(2~{R},3~{R},4~{R},5~{R})-2-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] hydrogen phosphate Mass: 692.427 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C₂₀H₂₆N₁₀O₁₄P₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.98 Å³/Da / Density % sol: 58.77 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 100 mM NaOAc pH 4.8, 10-11% PEG-20,000

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Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 19, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.1→38.281 Å / Num. obs: 81341 / % possible obs: 99.2 % / Redundancy: 3.5 % / CC_1/2: 0.999 / R_pim(I) all: 0.035 / Net I/σ(I): 9.9
Reflection shell	Resolution: 2.1→2.14 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4327 / CC_1/2: 0.847 / R_pim(I) all: 0.681 / % possible all: 97.2

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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: 2.1→38.281 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.31

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2239	1990	2.46 %	10
R_work	0.1994	-	-	-
obs	0.2	80834	98.45 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.1→38.281 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7762	0	230	202	8194

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	8217
X-RAY DIFFRACTION	f_angle_d	0.885	11178
X-RAY DIFFRACTION	f_dihedral_angle_d	13.101	4691
X-RAY DIFFRACTION	f_chiral_restr	0.058	1185
X-RAY DIFFRACTION	f_plane_restr	0.005	1386

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 (%)
2.1001-2.1527	0.4061	136	0.423	5409	X-RAY DIFFRACTION	95
2.1527-2.2109	0.3521	140	0.3703	5522	X-RAY DIFFRACTION	98
2.2109-2.2759	0.3446	140	0.3197	5587	X-RAY DIFFRACTION	98
2.2759-2.3494	0.3397	142	0.3079	5539	X-RAY DIFFRACTION	98
2.3494-2.4333	0.3161	141	0.2853	5606	X-RAY DIFFRACTION	99
2.4333-2.5307	0.3159	142	0.2669	5605	X-RAY DIFFRACTION	98
2.5307-2.6459	0.2755	143	0.2485	5648	X-RAY DIFFRACTION	99
2.6459-2.7853	0.2638	142	0.2418	5639	X-RAY DIFFRACTION	99
2.7853-2.9598	0.3183	142	0.2381	5627	X-RAY DIFFRACTION	99
2.9598-3.1882	0.2556	142	0.2213	5630	X-RAY DIFFRACTION	98
3.1882-3.5088	0.2399	144	0.2033	5693	X-RAY DIFFRACTION	100
3.5088-4.0161	0.2197	145	0.1752	5762	X-RAY DIFFRACTION	100
4.0161-5.058	0.1606	144	0.1412	5750	X-RAY DIFFRACTION	100
5.058-38.2871	0.1527	147	0.1542	5827	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	3.7011	0.0765	-0.1073	3.0124	-0.2273	2.7573	0.1712	-0.004	-0.2295	-0.0563	-0.0911	-0.1908	0.3197	0.0901	0.0039	0.3942	0.0959	-0.0139	0.545	0.0002	0.503	17.3877	-2.4148	49.1455
2	5.274	1.1202	0.2044	3.5883	-0.5967	3.504	-0.0949	-0.4478	0.7931	0.0712	-0.1565	-0.1346	-0.2607	0.0547	0.156	0.4735	0.0187	-0.0052	0.479	-0.0042	0.6106	14.7524	16.83	51.1064
3	5.0014	1.2656	0.4907	3.2074	-0.66	3.6803	0.0763	0.8454	-0.1738	-0.2585	-0.1721	-0.5604	0.2193	0.015	0.0598	0.43	0.0214	0.0149	0.6654	-0.0772	0.4858	7.0269	1.2599	41.2413
4	6.1715	-0.2978	-0.5678	3.8198	0.4868	3.8316	0.2307	0.8626	1.2304	-0.7242	-0.2374	-0.9461	-0.7749	1.033	0.1091	0.6404	-0.0456	0.0188	0.7368	0.0991	0.7499	19.0044	14.9458	42.0194
5	6.2136	0.1565	1.8547	2.7852	-0.3392	3.9633	-0.1061	0.3765	0.3774	-0.026	-0.1068	-0.3108	-0.2982	0.3763	0.0878	0.4483	0.005	0.0362	0.5751	0.0732	0.6724	18.3261	11.4155	47.8546
6	6.304	0.8698	-1.0615	1.2323	0.0047	2.8606	-0.0055	0.4603	0.4585	-0.0222	0.0127	0.1488	-0.1801	-0.3003	-0.0391	0.4086	0.047	-0.0349	0.5213	0.0165	0.478	9.3454	9.9844	47.2429
7	4.7682	0.0275	0.5323	2.3875	-0.2025	2.7886	0.201	0.9611	-0.3473	-0.5994	-0.1475	-0.0303	0.3611	-0.0541	-0.0846	0.4867	0.0775	-0.0632	0.6225	-0.0705	0.4987	0.5385	-1.6995	36.3297
8	4.7174	0.5157	0.977	4.0902	1.1026	2.9038	0.3609	1.3668	0.5102	-1.292	-0.3367	0.0506	-0.272	-0.1633	0.0479	0.5881	0.113	-0.078	0.8786	0.0651	0.5504	-10.93	10.037	31.6758
9	4.2291	0.8088	0.7002	3.3048	0.8323	1.4935	-0.1853	1.5623	-0.6958	-0.8445	0.0286	2.0964	0.0558	-1.2001	-0.0067	0.639	0.1339	-0.1332	1.0027	-0.0231	0.6343	-21.0269	5.2916	31.566
10	4.2176	0.3425	0.2801	1.4048	0.2791	1.7703	0.1456	0.9741	-0.6271	-0.5178	-0.241	0.2421	0.3528	-0.0312	-0.0652	0.5439	0.0423	-0.0443	0.6671	-0.0538	0.639	-8.026	-2.219	34.2356
11	4.9402	0.1944	0.6486	1.2109	0.2417	2.2638	0.0835	0.807	-0.1464	-0.3042	0.0365	0.1198	0.0835	-0.2035	-0.0023	0.4811	0.045	-0.0516	0.6131	-0.0533	0.4341	-5.8141	4.8375	38.2378
12	4.0441	-0.4542	-0.7255	2.4679	0.4338	1.9756	0.2252	0.3973	-0.0074	-0.1537	-0.1977	0.4182	-0.1183	-0.2333	0.0884	0.4085	0.0142	-0.0589	0.6207	0.0081	0.6127	-26.3737	10.2322	46.4455
13	4.0897	-1.3104	-0.5267	2.9215	0.9124	3.1045	-0.1261	-0.228	0.064	0.1154	0.0486	0.012	0.0985	-0.0095	-0.0286	0.3788	-0.016	0.0104	0.5264	0.0023	0.5198	-17.2051	9.8687	56.7266
14	5.7183	-0.6318	-0.9818	3.5754	0.7539	4.2148	0.4933	-1.2128	0.1056	0.6433	0.0562	0.3492	0.0081	-0.4406	0.0489	0.53	-0.0042	0.0413	0.7727	0.022	0.6858	-23.6777	10.3869	65.0774
15	6.0896	-2.1656	0.4412	4.3006	-0.0091	3.1697	-0.1203	-0.4108	0.517	0.7341	0.116	0.4103	-0.353	0.0954	-0.0248	0.4795	0.0031	0.0625	0.6255	-0.0767	0.6237	-22.8962	14.0836	59.4868
16	5.5054	-0.7851	-1.6134	2.3461	-0.2211	2.528	0.031	-0.1198	-0.0831	-0.0356	-0.3323	-0.0441	0.0301	0.3416	-0.0294	0.415	-0.0048	-0.0267	0.478	0.052	0.5481	-15.2878	10.0815	56.4289
17	4.5288	-0.9757	-0.2348	2.4428	0.2773	1.2446	-0.012	0.0976	-1.0642	-0.4822	-0.0899	0.3998	0.4672	-0.2691	-0.0479	0.5667	-0.0291	-0.0796	0.5347	-0.0487	0.6925	-13.4243	-6.4463	48.9383
18	5.5937	-1.1207	-0.3589	3.021	0.8514	1.9202	-0.1483	-0.2215	-1.2407	0.1981	-0.0731	0.3051	0.493	0.0372	-0.0108	0.558	0.012	-0.0644	0.4754	0.0362	0.7055	3.9011	-12.9428	55.4611
19	4.164	-1.3765	-0.5253	1.65	0.8557	1.1501	0.0367	0.5584	-1.0861	-0.0676	0.0709	0.2148	0.6824	0.4456	0.0364	0.5982	0.0372	-0.0689	0.6654	-0.0781	0.6896	-6.1882	-11.3126	47.4574
20	2.1902	-0.57	-0.0788	3.2394	1.1573	2.0161	0.0603	-0.024	-0.592	0.016	-0.0699	0.153	0.4795	-0.1341	0.0336	0.4951	-0.0213	-0.0505	0.4214	-0.0202	0.562	-5.0277	-4.6381	52.4073
21	4.5798	1.362	-1.2217	3.1569	0.1844	3.9354	-0.1099	0.1078	0.2333	-0.1453	0.1505	0.1812	-0.2295	0.1466	-0.0665	0.3871	-0.0419	0.0164	0.5649	-0.0314	0.5676	1.5281	33.8053	73.921
22	6.5855	1.0382	-0.6875	2.9628	-0.619	4.3906	-0.1703	-0.1625	-0.1833	-0.1505	0.1739	-0.1882	0.1987	0.5659	0.0501	0.4182	-0.0616	0.0451	0.6134	-0.0401	0.544	2.4362	27.7679	76.4138
23	4.352	0.6697	-1.0881	2.5883	-0.9991	4.5537	0.0827	-1.4395	-0.5743	0.7748	-0.2111	-0.1765	0.0696	0.6109	0.0912	0.5754	-0.0501	0.0123	1.0111	0.1421	0.5909	-6.6954	21.0526	97.6456
24	3.629	0.9319	-0.0909	2.3491	-0.3215	3.0427	0.0675	-0.531	-0.3484	0.2713	-0.1192	0.1618	0.3204	0.1283	0.0639	0.5605	-0.0266	0.1621	0.8135	-0.0033	0.6962	-30.9907	19.6953	91.249
25	4.0891	1.6175	-0.6036	2.9549	-0.0412	1.6318	0.2918	-0.8809	0.6117	0.2356	-0.2185	0.3313	-0.2749	-0.1523	-0.0689	0.5461	-0.0353	0.1661	0.8274	-0.1775	0.6352	-21.7482	33.9647	92.2926
26	3.3922	1.069	-0.8666	2.3698	-0.3371	2.4421	0.179	-0.996	0.5839	0.3584	0.0902	-0.1209	-0.6397	-0.0782	-0.0473	0.6312	-0.0478	0.0976	0.8304	-0.211	0.6835	-13.918	37.9016	91.4728
27	2.2739	0.5286	2.3468	0.4336	0.7069	2.8076	-0.1584	-1.1372	-0.2713	1.1498	0.3123	-0.1154	-1.1393	-0.6322	-0.5136	0.7475	0.1301	0.1856	1.1021	0.1161	0.8253	-17.6183	24.7272	20.4207
28	3.3059	1.0404	-0.5029	2.66	-0.5964	4.2213	-0.097	-0.0059	-0.3562	0.3291	0.0445	0.1442	0.1314	-0.0879	0.018	0.6351	0.0737	0.173	1.0092	-0.0339	0.7239	-13.1431	17.8123	12.3483
29	4.2165	-0.8112	-1.112	4.4736	-0.5994	4.9151	-0.0041	0.4686	-0.0825	0.0762	0.1269	0.5822	0.1369	-0.674	-0.0307	0.5679	0.0111	0.1842	1.0192	0.0075	0.7058	-17.3847	20.289	8.0525
30	3.5512	-0.0203	-1.5372	1.3762	-0.604	4.2955	0.2059	0.8178	0.352	-0.1585	-0.0376	0.2267	-0.5113	-0.3043	-0.1858	0.6875	0.1355	0.1046	1.0356	0.056	0.6754	-9.5136	29.5732	-3.8734
31	2.3803	0.1597	-1.604	1.1385	0.0817	2.9565	0.4407	0.9988	0.7793	-0.3779	-0.2137	0.0362	-1.2377	-0.4318	-0.4509	0.9948	0.1288	0.2057	1.3043	0.1988	0.811	-1.9347	37.9166	-13.4205
32	3.1942	-0.0511	-2.255	2.0606	-1.063	4.0218	0.1646	1.0593	0.5017	-0.2739	0.0482	0.0977	-0.7175	-0.5823	-0.2201	0.7562	0.1154	0.1462	0.9342	0.1104	0.6726	-5.461	30.5599	-6.5454

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 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 108 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 109 through 124 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 125 through 137 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 138 through 150 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 151 through 164 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 165 through 194 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 0 through 29 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 30 through 66 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 67 through 79 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 80 through 98 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 99 through 108 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 109 through 124 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 125 through 150 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 151 through 164 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 165 through 194 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 1 through 49 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 50 through 108 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 109 through 195 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 0 through 49 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 50 through 163 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 164 through 194 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 0 through 9 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 10 through 49 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 50 through 98 )
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 99 through 137 )
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 138 through 164 )
32	X-RAY DIFFRACTION	32	chain 'E' and (resid 165 through 194 )

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