PDB-9wha: Crystal Structure of Bovine STING bound to 2'3'-cGAMP

ID or keywords:

Entry

Database: PDB / ID: 9wha

Title

Crystal Structure of Bovine STING bound to 2'3'-cGAMP

Components

Stimulator of interferon genes protein

Keywords

SIGNALING PROTEIN / STING / 2'3'-cGAMP

Function / homology

Function and homology information

STING mediated induction of host immune responses / STAT6-mediated induction of chemokines / IRF3-mediated induction of type I IFN / Regulation of innate immune responses to cytosolic DNA / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / cGAS/STING signaling pathway / proton channel activity / Neutrophil degranulation / reticulophagy ...
Similarity search - Function

Biological species

Bos taurus (domestic cattle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Zhao, Z.Z. / Li, X.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Species-Specific Regulation of STING by a C195 Disulfide Tetramer in Duck
Authors: Zhao, Z.Z. / Li, X.

History

Deposition	Aug 26, 2025	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Mar 4, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9wha.cif.gz	173.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9wha.ent.gz	136.8 KB	Display	PDB format
PDBx/mmJSON format	9wha.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/wh/9wha ftp://data.pdbj.org/pub/pdb/validation_reports/wh/9wha	HTTPS FTP

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Related structure data

Related structure data	9wh7C 9wh8C 9wh9C 9whfC C: citing same article (ref.)
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: Stimulator of interferon genes protein

B: Stimulator of interferon genes protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	50.729, 57.910, 132.269
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Stimulator of interferon genes protein / STING / Transmembrane protein 173 Mass: 22249.025 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: STING1, STING, TMEM173 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2KI99
#2: Chemical	ChemComp-1SY / cGAMP / 2',3' cGAMP / c-GMP-AMP / c[G(2',5')pA(3',5')p] Mass: 674.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₀H₂₄N₁₀O₁₃P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.15 Å³/Da / Density % sol: 42.85 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1M Sodium acetate trihydrate pH4.6, 2M Sodium chloride

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 12, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.6→66.13 Å / Num. obs: 52228 / % possible obs: 99.8 % / Redundancy: 11.2 % / CC_1/2: 0.991 / Net I/σ(I): 7.5
Reflection shell	Resolution: 1.6→1.63 Å / Num. unique obs: 2542 / CC_1/2: 0.953

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Processing

Software

Name	Version	Classification
PHENIX	(1.17.1_3660: ???)	refinement
XDS		data scaling
XDS		data reduction
PHENIX		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→53.05 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.65 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2413	2556	4.93 %
R_work	0.216	-	-
obs	0.2172	51886	99.26 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.6→53.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2972	0	45	284	3301

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	3136
X-RAY DIFFRACTION	f_angle_d	0.687	4275
X-RAY DIFFRACTION	f_dihedral_angle_d	20.625	1139
X-RAY DIFFRACTION	f_chiral_restr	0.046	462
X-RAY DIFFRACTION	f_plane_restr	0.003	557

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 (%)
1.6-1.63	0.3719	143	0.3569	2661	X-RAY DIFFRACTION	99
1.63-1.66	0.3103	141	0.3233	2677	X-RAY DIFFRACTION	98
1.66-1.7	0.3624	135	0.2928	2694	X-RAY DIFFRACTION	99
1.7-1.74	0.3667	152	0.2786	2674	X-RAY DIFFRACTION	99
1.74-1.78	0.3045	158	0.2736	2657	X-RAY DIFFRACTION	99
1.78-1.83	0.2597	143	0.2601	2705	X-RAY DIFFRACTION	98
1.83-1.89	0.2605	136	0.2525	2720	X-RAY DIFFRACTION	99
1.89-1.95	0.2811	133	0.234	2715	X-RAY DIFFRACTION	99
1.95-2.02	0.2508	153	0.2136	2714	X-RAY DIFFRACTION	100
2.02-2.1	0.2439	150	0.2073	2713	X-RAY DIFFRACTION	100
2.1-2.19	0.2339	140	0.2076	2738	X-RAY DIFFRACTION	100
2.19-2.31	0.2289	144	0.2076	2752	X-RAY DIFFRACTION	100
2.31-2.45	0.2483	135	0.2142	2757	X-RAY DIFFRACTION	100
2.45-2.64	0.2514	142	0.2138	2789	X-RAY DIFFRACTION	100
2.64-2.91	0.261	151	0.2169	2754	X-RAY DIFFRACTION	100
2.91-3.33	0.2097	137	0.2036	2814	X-RAY DIFFRACTION	100
3.33-4.19	0.1903	137	0.1806	2839	X-RAY DIFFRACTION	100
4.19-53.05	0.2155	126	0.1986	2957	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	5.7725	-2.3545	3.3526	6.5743	-2.048	7.7276	-0.2608	-0.2365	0.2582	0.2634	0.3109	-0.0306	-0.9452	-0.2878	-0.0445	0.2218	-0.0205	0.051	0.1644	-0.0165	0.1375	-9.7369	11.3155	-17.1477
2	1.9629	-2.9583	-0.8658	6.4496	1.34	2.9687	0.337	-0.0141	0.1435	-0.8212	-0.0556	-0.5907	0.0065	0.4463	-0.1921	0.2497	0.0423	0.0427	0.1938	-0.0206	0.2071	1.6568	-5.8718	-27.4458
3	2.5355	-1.2324	1.556	3.4336	-0.4664	5.1707	0.0196	0.0671	-0.2113	-0.2455	0.1367	0.3433	0.1457	-0.3502	-0.1723	0.1928	-0.0434	0.0165	0.1599	0.0016	0.1547	-13.0501	-2.5746	-29.8513
4	0.6389	-0.4677	1.3723	1.4447	-0.0806	7.0275	0.181	0.0312	-0.0615	0.0174	0.1481	0.0789	0.4633	0.1708	-0.3308	0.2003	-0.0437	0.0088	0.1442	-0.0047	0.1776	-8.9344	-5.3396	-23.3039
5	2.772	-1.103	-0.0145	3.563	0.4607	3.7501	-0.1592	-0.2444	0.0296	0.0369	0.1241	0.4538	-0.4658	-0.7898	0.0748	0.2464	0.0744	-0.0363	0.3045	0.0488	0.2076	-19.1186	5.4431	-26.176
6	8.6768	-4.0208	1.0868	5.7829	-1.1471	5.1868	0.5163	0.3231	0.1344	-0.3781	-0.1622	0.3831	-1.2288	-0.4616	-0.2328	0.7115	0.0768	0.0401	0.2181	0.022	0.2667	-13.8333	16.9732	-25.3104
7	2.4201	0.6773	0.9668	6.7254	0.9776	3.3856	-0.2023	0.2295	0.4371	0.0556	0.1416	-0.7885	-0.7442	0.6622	0.1061	0.3913	-0.1083	0.0187	0.2648	-0.0084	0.2425	-2.1071	8.057	-28.1623
8	7.764	-2.6233	0.9366	4.4011	-3.6847	3.3438	0.2326	0.6227	-0.3443	-1.4297	-0.6668	2.7784	-0.7779	-2.6469	0.5298	0.6225	0.1665	-0.2344	0.7844	-0.0979	0.7441	-22.0936	8.5641	-41.94
9	2.3124	1.0421	-2.6538	5.464	-0.0994	6.2815	-0.018	0.1045	0.0317	-0.413	0.0082	-0.4561	-0.2431	0.6547	0.0689	0.4237	-0.0793	0.0291	0.2729	0.0116	0.2021	-3.253	4.3692	-41.4959
10	1.1121	0.2327	-0.71	7.4775	2.8849	6.9051	0.0973	-0.0531	0.0563	-0.5423	0.2334	0.4284	-0.9032	0.0758	-0.1532	0.0992	0.1186	0.001	0.4814	0.0349	0.2335	-21.2412	8.7161	-12.1101
11	3.6483	-2.8585	3.3313	5.0069	-6.3054	8.6213	0.1918	0.006	-0.3952	-0.4807	0.1329	0.561	0.5982	-0.6544	-0.3771	0.2333	-0.0721	-0.0028	0.4254	-0.0019	0.2193	-24.0863	-11.0845	-6.5609
12	1.3222	-1.8393	2.6099	2.9577	-3.1432	7.7989	0.1665	-0.3816	-0.3999	0.763	0.2696	0.8415	0.6274	-0.2394	-0.3461	0.4997	-0.1089	0.0459	0.5133	0.0763	0.367	-23.5105	-13.2245	3.8422
13	6.557	4.6272	1.3551	6.0663	-1.0022	4.8736	-0.0433	-0.1395	-0.0659	0.0199	-0.0433	-0.1047	-0.2489	-0.1092	0.0644	0.2063	0.045	0.038	0.2064	-0.0102	0.1408	-12.7281	4.6161	0.1586
14	7.3493	2.9888	5.9506	4.9072	3.778	5.3938	0.2257	0.1674	-0.1225	0.1899	0.063	-0.3052	0.7224	0.3326	-0.254	0.1607	0.0314	0.0672	0.2481	0.0465	0.1581	-11.3748	-8.6573	-0.194
15	4.5026	2.8984	-2.8127	8.4468	-6.6669	6.6039	-0.3427	-0.2024	-0.3176	-0.6584	0.1697	0.1646	0.4386	0.0311	0.0492	0.206	0.0798	0.0199	0.2852	0.0297	0.1897	-15.9808	-5.755	-19.025
16	1.9888	1.2503	0.2154	3.6499	0.7841	9.1358	0.0313	-0.1905	-0.1092	0.388	0.1522	0.0488	0.617	-0.2768	-0.1744	0.1772	0.0255	0.0242	0.2323	0.0132	0.1594	-14.2678	-7.1527	7.1588
17	9.036	4.8875	0.5716	6.98	-1.2817	3.8954	-0.2659	0.1366	0.2867	-0.3711	0.1384	-0.3055	-0.3861	0.2034	0.141	0.3362	-0.007	0.0352	0.2203	-0.0357	0.2164	-6.7842	15.2869	-8.6563
18	9.2747	5.1367	2.9631	5.6282	1.7962	2.8372	0.1747	0.1802	0.9411	0.4643	-0.11	0.6722	-0.4211	-0.3975	0.0272	0.4134	0.2081	0.0928	0.3683	0.0295	0.3156	-19.7828	15.3613	-3.6573
19	2.9872	-0.8659	-2.3541	7.4399	-1.2113	2.9155	-0.1556	0.0473	0.0951	-0.3207	-0.1017	0.975	-0.0698	-1.5281	0.1937	0.2274	0.0604	0.0504	0.5597	-0.0108	0.2666	-26.5114	2.1323	-1.4902
20	6.8926	7.3858	-6.1897	9.2222	-5.7707	6.1526	0.0076	0.4227	0.7164	-0.0023	-0.4346	-1.4815	-0.843	0.9458	0.5598	0.4432	-0.0377	0.0037	0.5016	0.1628	0.5531	-7.3299	9.2324	10.4802
21	0.9113	1.6756	0.6537	8.9806	-0.3994	4.2371	0.3552	-0.5252	0.2332	0.2821	-0.3572	0.8836	-0.2083	-1.147	-0.0137	0.2711	0.0661	0.0473	0.5336	-0.0373	0.2279	-22.7908	-0.1633	11.5009

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 155 through 167 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 168 through 197 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 198 through 230 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 231 through 251 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 252 through 280 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 281 through 301 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 302 through 314 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 315 through 324 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 325 through 341 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 155 through 167 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 168 through 185 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 186 through 197 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 198 through 211 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 212 through 230 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 231 through 242 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 243 through 262 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 263 through 280 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 281 through 301 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 302 through 314 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 315 through 324 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 325 through 340 )

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