PDB-7ebd: Bacterial STING in complex with c-di-GMP

ID or keywords:

Entry

Database: PDB / ID: 7ebd

Title

Bacterial STING in complex with c-di-GMP

Components

TIR-like domain-containing protein

Keywords

SIGNALING PROTEIN /

second messenger /

complex / cyclic dinucleotide / antiviral pathway

Function / homology

CD-NTase-associated protein 12/Pycsar effector protein, TIR domain / CAP12/Pycsar effector protein, TIR domain /

ACETATE ION / Chem-C2E / TIR-like domain-containing protein

Function and homology information

Biological species

Prevotella corporis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.25 Å

Authors

Ko, T.-P. / Wang, Y.-C. / Yang, C.-S. / Hou, M.-H. / Chen, Y.

Funding support

Taiwan, 1items

Citation

Journal: Nat Commun / Year: 2022
Title: Crystal structure and functional implication of bacterial STING.
Authors: Ko, T.-P. / Wang, Y.-C. / Yang, C.-S. / Hou, M.-H. / Chen, C.-J. / Chiu, Y.-F. / Chen, Y.

History

Deposition	Mar 9, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 15, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 19, 2022	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7ebd.cif.gz	176.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7ebd.ent.gz	122 KB	Display	PDB format
PDBx/mmJSON format	7ebd.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/eb/7ebd ftp://data.pdbj.org/pub/pdb/validation_reports/eb/7ebd	HTTPS FTP

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Related structure data

Related structure data	7eblC C: citing same article (ref.)
Similar structure data	6odc-2 4ffp-d 6lye-d 3ewf-5 4qa5-2 4ffr-d 7mos-1 5b25-1 5b25-2 6odc-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#130 - Oct 2010 Riboswitches similarity (1)

Deposited unit

A: TIR-like domain-containing protein

B: TIR-like domain-containing protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: homology

Unit cell

Length a, b, c (Å)	94.534, 86.995, 35.223
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x+1/2,y+1/2,-z #4: -x,-y,z

Components on special symmetry positions

ID	Model	Components
1	1	B-624- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	chain 'A'	A	157 - 182
1	2	1	chain 'A'	A	184 - 201
1	3	1	chain 'A'	A	203 - 213
1	4	1	chain 'A'	A	216 - 227
1	5	1	chain 'A'	A	229 - 252
1	6	1	chain 'A'	A	254 - 265
1	7	1	chain 'A'	A	267 - 286
1	8	1	chain 'A'	A	288 - 313
2	9	1	chain 'B'	B	157 - 182
2	10	1	chain 'B'	B	184 - 201
2	11	1	chain 'B'	B	203 - 213
2	12	1	chain 'B'	B	216 - 227
2	13	1	chain 'B'	B	229 - 252
2	14	1	chain 'B'	B	254 - 265
2	15	1	chain 'B'	B	267 - 286
2	16	1	chain 'B'	B	288 - 313

#1: Protein	TIR-like domain-containing protein / STING Mass: 18631.123 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Prevotella corporis (bacteria) / Gene: HMPREF3226_02659 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A133PTK7
#2: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate / Cyclic di-GMP Mass: 690.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₀H₂₄N₁₀O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 1.98 Å³/Da / Density % sol: 37.83 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1M sodium cacodylate trihydrate pH 6.5, 0.2M sodium acetate trihydrate, 18% w/v polyethylene glycol 8000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.97836 Å
Detector	Type: RAYONIX MX300-HS / Detector: CCD / Date: Aug 20, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97836 Å / Relative weight: 1
Reflection	Resolution: 2.25→30 Å / Num. obs: 14459 / % possible obs: 99.8 % / Redundancy: 9.3 % / B_iso Wilson estimate: 27.66 Å² / R_merge(I) obs: 0.106 / R_pim(I) all: 0.036 / Net I/σ(I): 22.6
Reflection shell	Resolution: 2.25→2.33 Å / Redundancy: 9 % / R_merge(I) obs: 0.615 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1410 / R_pim(I) all: 0.215 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.25→21.78 Å / SU ML: 0.2162 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.777 / Stereochemistry target values: GeoStd + Monomer Library

	R_factor	Num. reflection	% reflection
R_free	0.2487	720	4.92 %
R_work	0.1883	25305	-
obs	0.1911	14413	99.69 %

Solvent computation

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

Displacement parameters

B_iso mean: 47.08 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→21.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2532	0	54	262	2848

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0021	2634
X-RAY DIFFRACTION	f_angle_d	0.5493	3564
X-RAY DIFFRACTION	f_chiral_restr	0.0402	404
X-RAY DIFFRACTION	f_plane_restr	0.0028	446
X-RAY DIFFRACTION	f_dihedral_angle_d	16.8338	1576

LS refinement shell

Resolution: 2.25→2.34 Å

	R_factor	Num. reflection	% reflection
R_free	0.3026	144	-
R_work	0.2748	1385	-
obs	-	-	98.37 %

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	0.462067574411	-0.107832113792	0.286903913869	0.112329773145	0.0306815569332	0.315527653392	-0.0898428924479	0.254234977108	-0.0688491428499	-0.0275280556975	-0.0881563198845	0.134092410861	0.025971357844	0.164722225639	-0.2187862662	0.11023644582	-0.0207168122783	0.0328387335071	0.075120940662	-0.00242650943272	0.116909106693	31.4937298255	20.8752778934	-7.7942712153
2	0.0127148192133	-0.0172053778402	0.00237988460515	0.108078625856	-0.0719089791086	0.0467402298834	-0.0595000562439	0.0140604980793	0.12140515488	-0.0804208613585	-0.0545545018725	-0.0108393550528	-0.00691908301325	-0.227120671076	-0.0152319700948	0.449024859521	0.052078437319	-0.052435784468	0.216822061522	0.0845340436201	0.41397427514	39.1797168255	40.7356327994	-10.2954181504
3	0.0391622725649	-0.00614985357876	0.00894611468327	0.0607312892384	0.05526081785	0.0306482696322	0.0464615866829	-0.107365376749	0.102759123147	0.0532424874825	-0.00899270541354	-0.135274698622	0.0378332389891	0.0360937606445	0.000196872936553	0.126175883982	-0.0224092847844	-0.00823453135222	0.179025240532	0.0146010943671	0.153003456297	39.668614137	21.2758522657	3.34221429082
4	0.0576869958817	-0.0627777596129	-0.00866111082217	0.0676419770244	0.0251908833469	0.149892270222	-0.179946653656	-0.00349233633268	-0.00438071400743	0.170574563494	-0.0650587338699	0.0239679379217	-0.145027236646	-0.0705308549974	-0.174041091813	0.471316543533	-0.0524448469081	-0.0282742883254	0.180361492802	0.00110415888836	0.068565265851	37.6962872561	26.912473915	10.4863307906
5	0.0147337254845	0.00826596235536	-0.00863757056358	0.0154280768062	-0.0141874474038	0.00512956380489	0.123010003149	0.0191799669194	-0.0602070987088	-0.0926679393088	-0.0157724966554	-0.0906682325362	-0.119344499093	0.00488921952097	-1.14451630041E-5	0.199512143675	-0.00107956332489	-0.0110932614807	0.23225947294	-0.0161043121954	0.366510282202	37.0956312472	34.9867736495	0.79270686221
6	0.0905686074817	-0.0425402505776	0.022334200711	0.112485598945	0.208380729889	0.403721272876	-0.0841053120131	-0.203773683768	0.207799799625	0.115175919091	-0.0039898971371	0.0247452011125	-0.318417544379	-0.239032640222	-0.0456444615899	0.146526109667	-0.012093690784	-0.0333381422068	0.103527833681	0.0322862838957	0.208286388799	35.5022385138	31.9530054162	-3.89233716784
7	0.00174929849119	0.00436654903716	0.00240561646085	0.00530158544417	-0.00406307655188	0.0143504195639	-0.0503141896367	-0.144970231856	-0.00141685313399	0.012900674426	0.0615315083272	-0.0428982693983	-0.0176817235296	-0.0206840278112	-0.00841504425624	0.0885814840622	0.0394682197199	-0.0134885048195	0.160326833852	0.070701330684	0.129890428127	28.5504820399	11.06976814	8.95619172579
8	-0.000441483059682	0.00141577176124	0.000620246959044	5.0276419923E-5	-0.00191538891015	0.000981465889411	-0.034633978735	-0.0839036191391	0.0580894727089	0.0161600739909	-0.0197696300442	-0.0214367754816	0.038191149838	0.0425474177693	2.16009819196E-5	0.897277810199	-0.00179146252062	-0.0618234029496	0.754013038055	0.193945464227	0.415012788299	32.9785871421	4.56554780059	18.7451247052
9	0.0355438465705	0.00631657520661	0.0200848641648	0.083055113163	0.0273131931757	0.0315688893125	-0.0485613349343	-0.309973038666	-0.122674764294	0.248934409642	0.120458727899	-0.212167903267	0.181698694818	0.20694010747	0.0710866469674	0.138858876506	0.231863615171	0.279499200552	-0.012650772553	-0.214086873653	0.00640250501283	37.8247367406	9.26961321309	0.375111665205
10	0.14235107353	0.0238603685173	0.0476097801783	0.0911095205566	0.0316661785968	0.0818435968124	-0.0265021889166	0.0727210971201	-0.164294925893	-0.293942049369	0.210560395889	-0.128657644313	-0.0485786992874	0.0796365499611	0.200343761775	-0.0763212769177	-0.120959289336	0.233952405402	0.150639015614	0.104765106779	-0.0558159669985	41.9638686838	21.097633581	-9.4408234396
11	0.186241382492	-0.0437550050447	0.116527866926	0.036557029273	-0.0722448681101	0.206909933572	-0.100371336635	-0.120058058801	-0.0538966341565	0.0601244892907	0.0531290089507	-0.0696838619752	-0.000835103049269	-0.0157421324715	-0.0695319765316	0.140216607121	-0.0134995903704	0.0155996142393	0.120645495694	0.000906785886604	0.134035802159	19.4306512141	20.6002013433	7.59686488624
12	0.00798358548345	0.0149584341383	-0.0220589138385	0.103137484459	-0.0935730475816	0.15245638438	-0.149578482548	-0.0223193848081	-0.0725221754209	-0.0601499671388	-0.142046884284	0.0908063213402	-0.235962141136	0.15767682238	-0.00680403843741	0.576909685833	-0.0427780220975	-0.044618688038	0.275794262542	-0.164605333675	0.446917978495	11.1295910496	39.9970986228	9.90747829688
13	0.0213837632772	-0.00408769439481	0.0214398707147	0.0119893541946	-0.0136739052204	0.161838608101	0.0162107407803	0.0037194376221	-0.0360670654165	-0.159777967159	-0.202468714146	0.0803817845617	0.162171810526	0.12848541212	-0.00684502858021	0.189252741919	0.00602043901981	-0.00388362560394	0.142548332248	-0.0201620134699	0.112576169009	11.1527813672	20.5722220562	-3.4501889463
14	0.0394606758378	0.0332984670805	-0.0159453109464	0.032412120122	-0.0169519070925	0.0105316616884	-0.144385459139	0.174852010705	-0.0202455519709	-0.218095976362	-0.066113156625	-0.0298068932972	-0.0510874346915	0.133271313013	-0.0272421134425	0.362434128733	0.0338384793261	-0.053820888409	0.36165108809	0.0175443515617	0.103208521685	12.793524984	26.3001203127	-10.5912417794
15	0.0218118664925	0.000747565695882	-0.0147120590659	0.0162570272158	0.0173773075918	0.0120030402971	0.0606250206018	-0.106020352447	-0.0439250649349	0.130140546987	-0.112955826141	0.141309555771	-0.154313484589	0.00514518129087	0.000122868099641	0.243079897132	-0.022251881243	-0.0349538309304	0.234615355201	0.0288671498028	0.380833672959	13.1395944581	34.3278847855	-0.997079036609
16	0.0606789953532	0.0833013496136	-0.0639160998421	0.102797221978	-0.081927429334	0.048267632218	0.111880584874	0.0750580866451	0.320245409959	0.0214253216065	-0.0170371470206	-0.185065084725	-0.171353556975	0.210448465957	0.00537740580829	0.14270160594	-0.0496333874116	-0.00360720429672	0.195367233265	-0.0247058804271	0.200254663558	14.8704819076	31.4728221824	3.72353500774
17	0.0248623010981	-0.0180835343755	-0.0337163479232	0.0065270740565	0.0183426922371	0.0443877516748	-0.0541951158153	0.217774526765	-0.0958418521701	-0.0802689223412	-0.00287310950018	0.0175201765392	0.0285957335916	-0.0369940780081	-0.0547941616385	0.0875199087982	-0.122227939079	-0.0464369482291	0.122562013845	-0.236414459487	0.0443553088651	22.722849617	12.0766927336	-8.81966788797
18	0.00247227774407	-0.00362830002616	-0.00109758014393	0.000957690428701	0.00161770706646	-0.000617744830543	-0.0249901513795	0.0111426153465	-0.00304759184891	-0.0437572492208	-0.000701231371171	-0.0674047049919	0.0576693716886	-0.000910233832643	1.98878961656E-5	1.37325210676	0.325369914426	-0.0454156452886	1.34531076593	0.232513136828	1.26381483941	19.4430925008	3.49888505031	-17.5562831852
19	0.0465641753899	-0.00487527144138	0.0451482701417	0.0318407151822	-0.00762253989893	0.0544847963833	-0.103364200341	0.355607121844	-0.316830188744	-0.103813064462	-0.00425649087604	0.22362311407	0.0433006380906	-0.136803631215	0.000916006537359	0.153678200871	-0.114541985927	0.0573800579467	0.0507459107869	-0.0273869566944	0.296028795758	13.5489349893	8.620842375	-0.741849643524
20	0.0205443051187	-0.0154539928878	-0.0179833643766	0.285088393812	-0.0278389476936	0.0327239397794	-0.133463762539	-0.0225748125009	-0.0762547059225	0.279191425056	-0.0102086428635	0.0716371174072	-0.0340719292092	-0.075178632918	0.0099595449864	0.0507287567254	0.0128190336218	0.094688136016	0.192212189309	-0.0657918707809	-0.208167222767	8.81247198002	20.3067325653	9.33338323278

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 157 through 181 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 182 through 194 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 195 through 209 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 210 through 220 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 221 through 228 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 229 through 254 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 255 through 267 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 268 through 276 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 277 through 299 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 300 through 314 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 157 through 181 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 182 through 194 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 195 through 209 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 210 through 220 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 221 through 228 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 229 through 254 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 255 through 266 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 267 through 276 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 277 through 299 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 300 through 314 )

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About Yorodumi

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Yorodumi