PDB-9xut: Crystal structure of MPXV poxin in complex with 3'3'-cGAMP

ID or keywords:

Entry

Database: PDB / ID: 9xut

Title

Crystal structure of MPXV poxin in complex with 3'3'-cGAMP

Components

Poxin-Schlafen

Keywords

VIRAL PROTEIN / Enzyme / 3'3'-cGAMP / degradation

Function / homology

Function and homology information

nuclease activity / 2',3'-cyclic GMP-AMP binding / symbiont-mediated suppression of host innate immune response / hydrolase activity
Similarity search - Function

Biological species

Monkeypox virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.81 Å

Authors

Huang, Y.X. / Zhao, B.Y.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Crystal structure of MPXV poxin in complex with 3'3'-cGAMP
Authors: Huang, Y.X. / Zhao, B.Y.

History

Deposition	Nov 25, 2025	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	May 27, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9xut.cif.gz	341.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9xut.ent.gz	276.7 KB	Display	PDB format
PDBx/mmJSON format	9xut.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/xu/9xut ftp://data.pdbj.org/pub/pdb/validation_reports/xu/9xut	HTTPS FTP

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Related structure data

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

Deposited unit

A: Poxin-Schlafen

B: Poxin-Schlafen

C: Poxin-Schlafen

D: Poxin-Schlafen

hetero molecules

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

1

A: Poxin-Schlafen

B: Poxin-Schlafen

hetero molecules

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

2

C: Poxin-Schlafen

D: Poxin-Schlafen

hetero molecules

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

Unit cell

Length a, b, c (Å)	54.180, 91.850, 93.660
Angle α, β, γ (deg.)	90.00, 90.32, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Poxin-Schlafen Mass: 22421.723 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Monkeypox virus / Gene: OPG188, MPXVgp165 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7H0DNF0
#2: Chemical	ChemComp-4BW / 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one / 3',3' cGAMP / c-GMP-AMP / c[G(3',5')pA(3',5')p] Mass: 674.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₀H₂₄N₁₀O₁₃P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 884 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.6 Å³/Da / Density % sol: 52.66 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1 M HEPES pH 7.5, 12% w/v Polyethylene glycol 3,350

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Data collection

Diffraction	Mean temperature: 100 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: Sep 15, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.81→54.18 Å / Num. obs: 81352 / % possible obs: 97.6 % / Redundancy: 6 % / CC_1/2: 0.996 / R_merge(I) obs: 0.139 / Net I/σ(I): 11.7
Reflection shell	Resolution: 1.81→1.86 Å / R_merge(I) obs: 0.492 / Num. unique obs: 5918 / CC_1/2: 0.557

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Processing

Software

Name	Version	Classification
PHENIX	(1.21.1_5286: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHENIX		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.81→54.18 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.35 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2162	3840	4.72 %
R_work	0.1841	-	-
obs	0.1856	81290	97.34 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.81→54.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6208	0	89	884	7181

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	6512
X-RAY DIFFRACTION	f_angle_d	0.817	8825
X-RAY DIFFRACTION	f_dihedral_angle_d	20.672	2433
X-RAY DIFFRACTION	f_chiral_restr	0.056	933
X-RAY DIFFRACTION	f_plane_restr	0.006	1117

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 (%)
1.81-1.83	0.3501	130	0.3121	2836	X-RAY DIFFRACTION	97
1.83-1.86	0.3464	154	0.3077	2798	X-RAY DIFFRACTION	97
1.86-1.88	0.3219	136	0.2835	2838	X-RAY DIFFRACTION	96
1.88-1.91	0.328	142	0.2755	2844	X-RAY DIFFRACTION	96
1.91-1.94	0.2569	124	0.255	2858	X-RAY DIFFRACTION	96
1.94-1.97	0.2685	110	0.2583	2847	X-RAY DIFFRACTION	97
1.97-2	0.2658	129	0.2448	2907	X-RAY DIFFRACTION	97
2-2.03	0.2693	156	0.2425	2773	X-RAY DIFFRACTION	97
2.03-2.07	0.3169	115	0.2312	2912	X-RAY DIFFRACTION	97
2.07-2.11	0.2376	147	0.2195	2836	X-RAY DIFFRACTION	97
2.11-2.15	0.2309	135	0.2029	2884	X-RAY DIFFRACTION	98
2.15-2.2	0.2421	154	0.1935	2835	X-RAY DIFFRACTION	98
2.2-2.25	0.2195	154	0.1817	2912	X-RAY DIFFRACTION	98
2.25-2.31	0.2227	133	0.1789	2873	X-RAY DIFFRACTION	98
2.31-2.37	0.2008	170	0.1731	2883	X-RAY DIFFRACTION	99
2.37-2.44	0.1999	151	0.1733	2856	X-RAY DIFFRACTION	98
2.44-2.52	0.2195	135	0.1692	2919	X-RAY DIFFRACTION	98
2.52-2.61	0.1906	130	0.158	2919	X-RAY DIFFRACTION	99
2.61-2.71	0.2024	122	0.1689	2938	X-RAY DIFFRACTION	99
2.71-2.84	0.2249	162	0.1703	2919	X-RAY DIFFRACTION	99
2.84-2.99	0.1974	150	0.1702	2893	X-RAY DIFFRACTION	99
2.99-3.18	0.2235	150	0.1594	2905	X-RAY DIFFRACTION	99
3.18-3.42	0.1872	116	0.1512	2931	X-RAY DIFFRACTION	99
3.42-3.76	0.1691	150	0.1486	2883	X-RAY DIFFRACTION	98
3.76-4.31	0.203	165	0.1404	2905	X-RAY DIFFRACTION	98
4.31-5.43	0.1419	156	0.1368	2853	X-RAY DIFFRACTION	96
5.43-54.18	0.1998	164	0.1767	2693	X-RAY DIFFRACTION	90

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	1.7278	0.2835	0.1311	1.1221	0.2201	1.5437	0.0181	0.0431	0.0786	-0.0811	-0.0686	-0.1974	0.052	0.206	0.0737	0.1141	-0.0074	0.0338	0.1383	0.0398	0.1878	40.7392	3.2348	42.2664
2	0.9018	-0.5054	0.1987	1.5335	-0.3288	0.5344	0.0326	0.0282	-0.0023	-0.1201	-0.0064	0.0255	0.0513	0.0525	-0.0262	0.0951	-0.0074	-0.0035	0.0494	-0.0112	0.0615	29.3617	-1.9521	47.4076
3	0.9369	0.1083	-0.0786	1.566	-0.5802	1.269	-0.0276	0.0214	0.0852	0.0483	0.2211	0.3772	-0.0328	-0.5879	-0.1084	0.0682	0.0061	0.0247	-0.0151	0.027	0.1837	7.1612	14.8226	43.1047
4	0.5045	-0.7145	0.2013	1.5219	-0.282	0.5976	0.0361	0.0487	-0.0678	0.0123	0.0209	0.0688	0.0237	0.0129	-0.0647	0.0961	-0.0018	0.0093	0.0437	-0.0035	0.0994	15.0156	7.9998	41.8815
5	1.2515	-0.2557	-0.0142	1.3924	0.0533	0.9887	0.0622	0.0195	-0.181	0.0234	0.02	0.2142	0.1988	-0.3742	-0.0706	0.1473	-0.0446	-0.0252	0.2311	-0.0147	0.1684	1.9776	-3.2654	24.8013
6	1.1214	-0.0494	0.1808	1.2091	0.3544	1.2838	0.0954	0.1845	-0.1305	-0.0603	-0.0302	0.0886	0.1833	-0.1905	-0.0512	0.1273	-0.0101	-0.0371	0.1712	-0.0202	0.1028	7.5669	-1.4498	21.5095
7	2.5049	-0.5563	-0.5239	1.8481	0.2676	2.0249	0.1033	-0.0051	0.1532	0.0365	0.0105	-0.3752	-0.0574	0.2816	-0.0915	0.1416	0.0223	0.0138	0.0944	-0.0038	0.1432	30.6979	11.5378	23.4952
8	1.2716	-0.0003	0.2506	1.0525	-0.0347	1.4935	0.128	-0.0355	0.0894	0.1824	-0.0672	-0.1795	0.0324	0.1061	-0.068	0.1009	-0.0084	0.0115	0.1011	0.0121	0.0947	24.2925	10.6163	27.3186
9	1.7458	0.1055	0.0449	1.0704	-0.0891	1.8101	0.0839	0.0177	0.0346	-0.0241	-0.1395	0.1763	-0.0131	-0.3493	0.0146	0.1056	-0.0121	-0.0195	0.2641	-0.0348	0.168	25.6551	-0.3986	-4.5305
10	1.2992	-0.4799	-0.2236	1.6715	0.3566	1.4085	0.1086	0.0055	0.1409	-0.0724	-0.0365	0.1392	-0.2528	-0.1916	-0.0614	0.1332	0.0109	0.029	0.1479	-0.022	0.1145	36.0992	6.7549	-1.1345
11	1.4228	0.2132	-0.2575	1.3815	0.4996	1.7425	0.0336	-0.169	0.2385	0.0356	0.0318	0.1081	-0.2597	-0.2829	-0.0472	0.1319	0.0382	0.0463	0.1977	-0.0339	0.1539	32.0051	10.0312	4.9051
12	0.8727	-0.8483	-0.2804	1.0787	-0.1803	1.3635	0.0462	0.0319	-0.0458	-0.127	0.0425	0.0517	0.012	-0.1547	-0.1015	0.0916	-0.0291	0.0093	0.1566	0.0024	0.1272	38.5481	-1.6371	-4.7716
13	1.7953	-0.0351	-0.3095	0.3078	-0.1463	1.5475	0.0229	-0.1411	-0.0661	0.2451	0.1142	-0.2821	0.0805	0.2888	-0.1439	0.1258	0.0261	-0.0427	0.169	-0.0532	0.1583	55.5275	-5.9156	1.2043
14	1.2321	0.8004	0.2467	4.0113	3.6502	3.6591	-0.1363	0.071	-0.2457	-0.3118	0.1772	-0.6813	0.4963	0.4792	-0.0549	-0.7908	0.0749	-0.1727	0.5045	-0.186	0.4298	66.6545	-11.6351	-4.036
15	1.2259	-0.0544	-0.1967	1.6496	0.3427	1.3207	0.0207	0.0269	-0.2583	-0.153	0.1686	-0.0946	0.0953	0.2079	-0.1141	0.1074	0.0144	-0.0132	0.1441	-0.0333	0.133	51.5422	-13.9723	-6.2121
16	1.0483	-0.582	-0.3035	1.7475	0.4129	1.2872	0.0526	0.0191	0.0561	0.0266	0.0731	-0.0835	0.0331	0.2544	-0.1069	0.1082	-0.0031	-0.0011	0.1532	-0.0418	0.0956	51.4933	-4.3677	-4.9409
17	1.8131	-0.2797	-0.6484	1.2705	-0.1502	1.3767	0.1041	-0.0997	-0.0229	0.0832	-0.1199	-0.2104	-0.1171	0.3022	-0.0133	0.114	-0.0145	-0.0505	0.311	0.0166	0.1581	68.4052	-0.4875	-20.0635
18	1.2839	-0.1828	-0.3005	1.4251	0.4242	0.9734	0.2804	-0.0437	0.4869	0.1059	-0.0574	-0.1276	-0.2691	0.1612	-0.1156	0.2353	-0.0713	0.0589	0.186	-0.0241	0.202	59.6414	15.8745	-24.3225
19	1.2369	0.1064	-0.0134	1.1795	-0.3052	1.3961	0.0834	0.013	0.068	-0.0104	-0.0649	-0.0768	-0.064	0.3058	-0.0279	0.0714	-0.0122	0.0248	0.1721	-0.0277	0.0734	57.8749	2.78	-25.0754
20	2.7209	0.1238	0.1886	3.3475	-0.4036	3.314	0.0613	0.0828	0.0808	-0.0827	0.0478	0.1921	-0.0386	-0.2057	-0.1184	0.0765	0.0095	-0.0185	0.1021	-0.0263	0.1015	34.6741	-4.2231	-25.6427
21	3.4933	0.3186	-0.1824	4.3468	-2.9113	3.7486	0.0673	-0.004	-0.3875	-0.058	0.1834	0.5479	0.3891	-0.5061	-0.099	0.1586	-0.0373	-0.0191	0.2408	-0.0013	0.2388	26.6404	-9.3881	-21.8801
22	2.7824	0.4797	-0.4013	3.6643	-0.6067	1.8462	-0.0514	-0.1549	-0.3759	0.1512	0.1996	0.681	0.1958	-0.1135	-0.1081	0.105	-0.0206	-0.0153	0.0993	-0	0.2238	40.6727	-10.0211	-19.1451
23	0.5539	0.6494	-0.0854	2.1383	-0.3358	0.427	0.0781	0.0704	-0.0882	0.0861	-0.0082	0.0234	0.1046	-0.1069	-0.0617	0.1369	-0.0282	-0.0202	0.1114	-0.0336	0.1432	42.9372	-5.3093	-19.7833

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 128 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 129 through 163 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 164 through 194 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 0 through 49 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 50 through 113 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 114 through 149 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 150 through 194 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 0 through 29 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 30 through 66 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 67 through 98 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 99 through 117 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 118 through 137 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 138 through 150 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 151 through 163 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 164 through 194 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 0 through 29 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 30 through 49 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 50 through 123 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 124 through 137 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 138 through 147 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 148 through 173 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 174 through 194 )

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