PDB-9wh7: Crystal Structure of Duck STING bound to 2'3'-cGAMP

ID or keywords:

Entry

Database: PDB / ID: 9wh7

Title

Crystal Structure of Duck 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

2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / reticulophagy / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / positive regulation of type I interferon production / endoplasmic reticulum-Golgi intermediate compartment membrane / activation of innate immune response / defense response to virus ...
Similarity search - Function

Biological species

Anas platyrhynchos (mallard)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.49 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	9wh7.cif.gz	174 KB	Display	PDBx/mmCIF format
PDB format	pdb9wh7.ent.gz	138.5 KB	Display	PDB format
PDBx/mmJSON format	9wh7.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/9wh7 ftp://data.pdbj.org/pub/pdb/validation_reports/wh/9wh7	HTTPS FTP

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Related structure data

Related structure data	9wh8C 9wh9C 9whaC 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

B: Stimulator of interferon genes protein

A: Stimulator of interferon genes protein

hetero molecules

44.8 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)	83.535, 83.535, 353.159
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

#1: Protein	Stimulator of interferon genes protein Mass: 22038.020 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anas platyrhynchos (mallard) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8B9TBW9
#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.: 52 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 4.05 Å³/Da / Density % sol: 69.64 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 1 M Ammonium sulfate, 0.1 M Bis-Tris pH5.5, 1% polyethylene glycol 3350

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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: 2.49→88.29 Å / Num. obs: 26681 / % possible obs: 99.7 % / Redundancy: 30.1 % / CC_1/2: 0.998 / Net I/σ(I): 13.5
Reflection shell	Resolution: 2.49→2.6 Å / Num. unique obs: 2860 / CC_1/2: 0.938

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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: 2.49→37.68 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.99 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2314	1340	5.07 %
R_work	0.1943	-	-
obs	0.1962	26426	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: 2.49→37.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3121	0	0	52	3173

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	3244
X-RAY DIFFRACTION	f_angle_d	0.525	4414
X-RAY DIFFRACTION	f_dihedral_angle_d	24.784	1172
X-RAY DIFFRACTION	f_chiral_restr	0.036	480
X-RAY DIFFRACTION	f_plane_restr	0.004	546

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 (%)
2.49-2.58	0.3404	116	0.2696	2352	X-RAY DIFFRACTION	96
2.58-2.69	0.3074	131	0.2644	2436	X-RAY DIFFRACTION	99
2.69-2.81	0.3038	147	0.2685	2422	X-RAY DIFFRACTION	99
2.81-2.96	0.3177	139	0.2647	2460	X-RAY DIFFRACTION	99
2.96-3.14	0.3073	122	0.2567	2473	X-RAY DIFFRACTION	100
3.14-3.38	0.3212	124	0.2353	2514	X-RAY DIFFRACTION	100
3.38-3.72	0.2784	142	0.1956	2498	X-RAY DIFFRACTION	100
3.72-4.26	0.196	137	0.1583	2548	X-RAY DIFFRACTION	100
4.26-5.37	0.1605	132	0.1431	2588	X-RAY DIFFRACTION	100
5.37-37.68	0.1834	150	0.1766	2795	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	4.7002	3.1689	-0.0711	5.6041	-0.6481	6.3209	-0.3277	-0.1244	-0.7585	-0.2347	0.617	0.367	1.5589	0.0324	-0.229	0.9062	0.0652	0.111	0.5004	0.1338	0.4434	-20.3055	-32.5084	-3.4569
2	4.7507	0.2567	0.2624	2.2299	0.833	1.9975	-0.0347	0.0393	0.1783	0.4003	0.4191	0.8201	-0.0969	-0.925	-0.6449	0.3585	0.0264	0.0141	0.4362	-0.041	0.3606	-28.5103	-17.6959	-13.924
3	4.4592	-2.5531	-0.7084	3.8493	-1.7296	5.2401	-0.0295	-0.1124	-0.1355	0.023	0.1924	0.1174	0.1123	-0.4842	-0.0858	0.4203	-0.0006	0.0186	0.3093	-0.0391	0.2579	-21.463	-15.9312	-21.3206
4	4.0793	-0.5098	-1.2876	2.399	-1.4797	6.7451	0.2182	-0.0697	0.0562	-0.1439	-0.1746	-0.1478	-0.248	0.9399	-0.0323	0.4728	0.0035	-0.0452	0.4524	-0.0461	0.2707	-12.4691	-14.9758	-10.6853
5	4.9794	3.0107	-3.4135	3.8842	-4.2354	4.4354	0.3002	-0.2849	-0.1534	0.1726	-0.0513	0.2179	0.1186	0.4197	-0.4071	0.4662	-0.0112	-0.0031	0.3575	-0.0384	0.3446	-22.6514	-15.5414	-5.0182
6	2.9268	-1.4817	3.1686	5.6959	-5.1326	8.6234	0.0414	-0.0881	-0.1944	-0.0917	-0.1459	-0.4238	0.7694	1.1113	0.0723	0.5715	0.2479	0.0843	0.666	-0.0503	0.3978	-8.4238	-23.4855	-8.3677
7	6.1823	-1.5773	0.0069	3.0142	-1.5648	5.2447	-0.0945	0.2216	-0.9725	-0.1765	0.0698	0.0218	1.3345	0.4019	-0.0587	1.0059	0.1695	0.0452	0.3622	-0.0577	0.4719	-16.0634	-33.5359	-11.8892
8	4.6691	1.5778	-0.2451	4.9136	-6.3381	9.7621	-0.2291	0.0044	-0.6325	-0.5147	-0.2502	-0.7899	0.8444	2.2673	0.6472	0.7317	0.3593	0.0436	1.1588	0.0649	0.5865	-0.1685	-25.2384	-18.3643
9	8.8109	-3.6409	1.7539	7.5411	-1.9915	3.3118	0.3587	0.4105	-0.4541	-0.2726	-0.3787	0.1103	1.6906	0.4157	-0.0241	0.5838	0.0923	0.0931	0.4167	0.0028	0.2976	-13.6749	-22.6612	-25.741
10	5.044	1.7141	-0.2023	1.6613	0.243	1.3393	-0.1116	-0.5578	-0.3368	-0.1718	-0.0407	-0.7808	0.9658	0.391	0.344	0.8826	0.1705	0.1838	0.6157	0.0162	0.4246	-13.6956	-29.7818	6.6686
11	8.082	-8.0216	-5.427	9.6978	6.7876	4.6101	0.0207	-0.3651	0.7833	0.4935	0.1684	-0.7141	-0.3792	0.6473	-0.4032	0.6158	-0.1112	-0.0453	0.5189	-0.0037	0.4191	-18.7548	-10.1153	19.5359
12	3.8109	-1.2505	-1.0852	1.3407	0.6545	5.1393	-0.0497	0.0778	-0.0242	0.1001	-0.0193	0.2032	0.263	-0.3823	0.1105	0.5442	-0.0287	0.0299	0.3447	0.0393	0.3115	-29.1765	-20.3258	12.8469
13	1.9158	-1.0173	0.1612	2.0243	1.7128	2.3194	0.0835	-0.4298	-0.2774	-0.0883	0.0316	-0.1205	0.3531	1.1244	-0.1216	0.4599	0.0498	-0.0179	0.4564	0.0132	0.2927	-20.5006	-14.4868	4.6227
14	9.3347	-2.4382	3.1417	3.38	3.0718	7.8143	-0.3965	-1.4762	-0.2189	1.0417	-0.2767	0.8743	-0.0406	-0.2756	0.5618	0.8007	-0.128	0.1714	0.4706	-0.0044	0.4495	-31.1594	-17.3035	23.0798
15	8.4891	3.4775	3.7627	7.6039	1.5802	5.8358	0.0047	0.077	-1.1418	0.0711	0.2997	-0.4598	1.6184	0.2457	-0.3611	1.1134	0.1323	0.1374	0.4363	0.0538	0.4632	-21.8426	-36.9312	8.3208
16	5.3772	0.7093	1.0685	2.6892	0.9059	3.0448	-0.1917	0.1525	0.0336	0.3083	0.2913	0.1609	0.6796	0.0722	0.0449	0.6634	0.0133	-0.0196	0.4978	0.0748	0.2771	-23.1483	-27.8661	19.916
17	2.4758	2.3858	0.0074	7.2749	-2.428	8.6586	0.8919	-0.878	-0.2644	1.191	-0.6777	-0.6149	0.452	0.6672	-0.2205	0.8009	-0.0511	0.0064	0.6597	0.1159	0.4478	-25.4676	-23.0903	27.9529

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 157 through 170 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 171 through 186 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 187 through 206 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 207 through 233 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 234 through 251 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 252 through 283 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 284 through 317 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 318 through 326 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 327 through 343 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 157 through 170 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 171 through 200 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 201 through 233 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 234 through 250 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 251 through 265 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 266 through 304 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 305 through 326 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 327 through 343 )

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