PDB-6wt4: Structure of a bacterial STING receptor from Flavobacteriaceae sp...

ID or keywords:

Entry

Database: PDB / ID: 6wt4

Title

Structure of a bacterial STING receptor from Flavobacteriaceae sp. in complex with 3',3'-cGAMP

Components

Bacterial STING

Keywords

IMMUNE SYSTEM / CBASS / cyclic dinucleotide receptor / CD-NTase / immune effector

Function / homology

Prokaryotic STING domain / Prokaryotic STING domain / defense response to virus / nucleotide binding / plasma membrane / Chem-4BW / CD-NTase-associated protein 13

Function and homology information

Biological species

Flavobacteriaceae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.78 Å

Authors

Morehouse, B.R. / Govande, A.A. / Millman, A. / Keszei, A.F.A. / Lowey, B. / Ofir, G. / Shao, S. / Sorek, R. / Kranzusch, P.J.

Citation

Journal: Nature / Year: 2020
Title: STING cyclic dinucleotide sensing originated in bacteria.
Authors: Morehouse, B.R. / Govande, A.A. / Millman, A. / Keszei, A.F.A. / Lowey, B. / Ofir, G. / Shao, S. / Sorek, R. / Kranzusch, P.J.

History

Deposition	May 1, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 9, 2020	Provider: repository / Type: Initial release
Revision 1.1	Sep 16, 2020	Group: Database references / Source and taxonomy / Structure summary Category: citation / entity_src_gen / struct Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct.pdbx_descriptor / _struct.title
Revision 1.2	Oct 28, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Oct 9, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6wt4.cif.gz	165.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6wt4.ent.gz	110.2 KB	Display	PDB format
PDBx/mmJSON format	6wt4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6wt4_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	6wt4_full_validation.pdf.gz	1.3 MB	Display
Data in XML	6wt4_validation.xml.gz	14.4 KB	Display
Data in CIF	6wt4_validation.cif.gz	19.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wt/6wt4 ftp://data.pdbj.org/pub/pdb/validation_reports/wt/6wt4	HTTPS FTP

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Related structure data

Related structure data	6wt5C 6wt6C 6wt7C 6wt8C 6wt9C C: citing same article (ref.)
Similar structure data	1xto-d 4z67-d 3jxp-d 4z60-d 6e13-d 4r7o-4 4z6x-d 2iqt-d 1odf-d 4z5z-d 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: Bacterial STING

B: Bacterial STING

hetero molecules

38.2 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)	121.848, 121.848, 48.160
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	79
Space group name H-M	I4
Space group name Hall	I4
Symmetry operation	#1: x,y,z #2: -y,x,z #3: y,-x,z #4: -x,-y,z #5: x+1/2,y+1/2,z+1/2 #6: -y+1/2,x+1/2,z+1/2 #7: y+1/2,-x+1/2,z+1/2 #8: -x+1/2,-y+1/2,z+1/2

#1: Protein	Bacterial STING Mass: 18669.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Flavobacteriaceae (bacteria) / Strain: Flavobacteriaceae sp. genome bin 11 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DUD7*PLUS
#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.: 1 / Source method: obtained synthetically / Formula: C₂₀H₂₄N₁₀O₁₃P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.37 Å³/Da / Density % sol: 48.06 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 2 M ammonium sulfate, 0.2 M sodium acetate pH 4.5

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 14, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.78→44.79 Å / Num. obs: 34093 / % possible obs: 99.9 % / Redundancy: 13.8 % / B_iso Wilson estimate: 37.2 Å² / CC_1/2: 0.999 / R_pim(I) all: 0.019 / Net I/σ(I): 17.3
Reflection shell	Resolution: 1.78→1.82 Å / Num. unique obs: 1916 / CC_1/2: 0.68 / R_pim(I) all: 0.531

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
XDS		data reduction
Aimless		data scaling
AutoSol		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.78→43.08 Å / SU ML: 0.231 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.7541
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2303	2003	5.9 %
R_work	0.1985	31926	-
obs	0.2004	33929	99.51 %

Solvent computation

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

Displacement parameters

B_iso mean: 52.57 Å²

Refinement step

Cycle: LAST / Resolution: 1.78→43.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2343	0	55	98	2496

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0031	2521
X-RAY DIFFRACTION	f_angle_d	0.6322	3421
X-RAY DIFFRACTION	f_chiral_restr	0.0427	385
X-RAY DIFFRACTION	f_plane_restr	0.0028	413
X-RAY DIFFRACTION	f_dihedral_angle_d	16.6047	923

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 (%)
1.78-1.82	0.341	139	0.2978	2225	X-RAY DIFFRACTION	98.38
1.82-1.87	0.3186	142	0.2837	2301	X-RAY DIFFRACTION	99.92
1.87-1.93	0.383	136	0.3086	2147	X-RAY DIFFRACTION	95.8
1.93-1.99	0.2902	144	0.2595	2292	X-RAY DIFFRACTION	99.92
1.99-2.06	0.2772	139	0.2363	2247	X-RAY DIFFRACTION	99.96
2.06-2.15	0.2444	143	0.217	2299	X-RAY DIFFRACTION	99.75
2.15-2.24	0.2609	144	0.219	2268	X-RAY DIFFRACTION	99.88
2.24-2.36	0.2629	142	0.2204	2272	X-RAY DIFFRACTION	99.63
2.36-2.51	0.2625	144	0.2231	2304	X-RAY DIFFRACTION	100
2.51-2.7	0.2501	145	0.2252	2288	X-RAY DIFFRACTION	100
2.7-2.97	0.3014	141	0.2324	2303	X-RAY DIFFRACTION	100
2.98-3.4	0.2069	148	0.212	2284	X-RAY DIFFRACTION	100
3.41-4.29	0.2244	143	0.1661	2323	X-RAY DIFFRACTION	99.96
4.29-43.08	0.1738	153	0.161	2373	X-RAY DIFFRACTION	99.96

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	0.0534177803375	0.0453841066885	-0.130861020638	0.127119551538	-0.172082907667	0.254915336442	-0.331403415162	0.261979687677	-0.232925825229	-0.0564120923438	0.383504339394	-0.109474825776	0.504253417571	-0.0869351907561	-0.000102356446217	0.499850957447	-0.0390364309974	-0.0149998856639	0.38552642579	-0.0153169857989	0.436499730637	35.1678536715	20.5466447186	28.7551287059
2	-0.000998081479824	-0.0997335909907	-0.0338489393302	-0.0544773981879	-0.11253460099	0.0508992638532	-0.180706167573	-0.538903780432	-0.0768888200839	0.0361505409603	-0.0435726791904	-0.373358802078	0.304204555356	-0.135892040095	-0.000247157004697	0.412372694415	0.0984686225195	-0.0160289277329	0.443473151341	-0.0177620108108	0.5620927393	59.2154185723	24.8452312818	28.6212075662
3	0.15784410041	0.222498052944	-0.160657849413	0.349972351574	-0.233637661546	0.152839860323	0.249881461586	-1.00918101136	0.0772520937552	0.492657216674	-0.190181329467	-0.769370970697	0.400975581061	0.311414112033	-0.0170163089197	0.42257892212	-0.0299530153524	-0.0941648553327	0.788406220052	-0.0258833260985	0.472014280904	51.8151717893	26.4285850407	39.7855313276
4	0.0214473738265	-0.046363596017	0.0104347259862	0.0531527629812	-0.0502135052765	0.00433579727075	0.225130834289	-0.742664446426	0.101274060444	0.330882833676	-0.189385533693	0.211283165882	-0.306619153369	-0.892109827944	0.0139581363901	0.461306175038	0.122809402888	-0.0309166024939	0.831627647283	-0.193558920944	0.430048496369	35.9407329797	28.1557616041	42.7377897434
5	-0.00263209984595	0.0334736956842	-0.0903233647954	0.0254678643792	-0.044790080655	0.0380316121831	-0.315442719401	-0.722471744079	-0.843720714211	0.223784400983	0.0612598589215	-0.169125077572	0.548220957646	-0.180102697318	0.000581581552541	0.60366019241	-0.00185570029958	-0.00860039433294	0.490295478613	0.0695056072457	0.621770118079	42.2401363678	15.1719890531	35.1113350166
6	0.642214222561	0.213852788344	-0.666474831379	0.418568009711	-0.41957661078	0.442957861286	-0.13578428086	-0.0145329847749	-0.480127543038	0.0355140599964	0.0826057045338	-0.265294961048	0.238264570237	0.324110473532	-0.282053787907	0.29044087825	-0.0128748112554	0.0522957058546	0.366642132794	-0.179748802619	0.382945790074	55.4304556583	32.4169093079	17.4003778822
7	0.792976014906	-0.0146360666647	0.263262262923	0.619493508152	-0.528612296633	0.429472433793	-0.124591858065	0.505793564432	0.290684895286	-0.0652368759479	0.0372152005161	-0.129251342389	-0.426732459101	-0.249371034518	-0.00694874785885	0.348071127951	-0.104343779883	0.000277326878159	0.443851109191	-0.136835562575	0.3405015381	51.7106224922	45.4282921161	16.9420352863
8	0.547789147971	0.0479120556028	0.607485560789	-0.10276002768	-0.00157104207483	0.470507293422	-0.218681053717	-0.0349059690982	0.0924369674158	-0.21822759464	0.177526800255	0.269909139584	-0.0773746696413	0.0675958961179	-8.19567246215E-5	0.409474131653	-0.0482037561718	-0.0674757990422	0.325646557085	-0.0600343253977	0.364204017705	40.7451167532	44.7405366281	14.0657932191
9	-0.0394740485051	0.0170355710874	-0.0986641553134	0.0290058291087	-0.11904567137	0.0150432272602	-0.675880118902	0.251403269379	-1.18908166672	0.137654442631	0.618660674032	0.259486788836	0.240606660714	0.265396395929	-0.000425095869927	0.542502722018	0.117860747449	-0.00263700833525	0.450454288228	-0.0934586863372	0.591853192018	49.7956175657	23.0877165489	16.5683305206
10	0.733636873297	-0.218805306304	0.146653892633	0.337847155082	-0.218090012533	0.0373495595399	0.105284817424	0.246472919719	-0.505468233453	-0.136595452844	0.191322442192	0.0309253658979	0.205604258485	0.25064581115	0.187935867302	0.354036637472	-0.0464058258575	-0.0359516098662	0.370454793884	-0.16723913394	0.283738966695	45.6663080269	38.9636666564	10.185013776
11	0.0282464900456	-0.0174534694619	-0.0288394218943	0.0292234195844	0.0172135303807	0.0484096753813	-0.27562004492	-0.522950139925	0.214261921648	0.146716952374	-0.0878918823705	0.178996374692	-0.58536709411	-0.28608190775	-0.0427732303222	0.424939334656	-0.00719624210867	-0.0150546620542	0.466225673365	-0.184885365124	0.317765937207	49.4227150202	42.677840664	34.0341527819
12	0.678446455086	-0.263584407448	0.219180252911	0.492014490779	-0.622100770938	0.651575857274	-0.347780347558	0.0645041861549	0.0142832321071	0.177206116183	-0.0429952448576	-0.332501062348	-0.305906279397	0.240469054976	-0.424869996402	0.339775642607	-0.0168310902181	-0.075638769652	0.400769232549	-0.121521719216	0.44098587852	58.9011274938	43.6543040596	23.4562041428
13	0.0323044509534	-0.0247853329671	0.0612929473938	0.0374018083448	-0.0452760035875	0.0580315829866	-0.307843303625	-0.482641909861	0.728171357176	-0.244481782453	0.542032343205	0.0495946973002	-0.744386591464	-0.0472991866143	-0.00023740058755	0.624822800695	-0.00123950548746	-0.00171692019037	0.62613546223	-0.01892514032	0.801980988887	51.1660418885	52.4383956781	13.3814457118
14	0.0606682887533	-0.0653095968119	-0.075092348718	0.0531417690781	0.115069231995	0.187688447303	-0.0887822539909	-0.460283688614	0.42898265413	0.029841937382	0.209219251905	0.207397912157	-0.030211848759	0.356281386051	-4.02054344105E-5	0.283784126364	0.0155962863536	0.00333684948293	0.523285804761	-0.0830418600341	0.327224815325	49.6305032615	33.2034328561	34.557028852
15	0.0850285651002	0.245674797759	0.104101192804	0.171819977716	0.111395441373	0.0772658509167	0.455590641531	-0.168721657193	0.406533800212	0.13932066218	0.0321116756857	0.391901890418	0.0349753353253	0.154839451193	-0.000264560394748	0.313115125049	-0.013588681716	0.03477614108	0.328502533471	-0.0252867264927	0.467370697794	34.0315614347	32.5362260228	32.6607522355
16	0.15493035041	0.145653338954	-0.343043406564	0.0125452358972	-0.222897471034	0.312951797084	0.0371137304525	-0.0912687756318	-0.303193693153	0.0138149719383	-0.0809494473021	0.0167828681477	0.409370504851	0.0542060540372	0.000129867403015	0.455629319428	0.0793996173313	-0.013127034816	0.410539393444	0.0774009571805	0.474886392133	43.4096497013	20.1555422309	33.0328921018
17	0.0290977456085	0.0181731955859	-0.139958449672	0.74755652344	-0.686579490376	1.33328383566	-0.157085285324	-0.0436182437339	-0.944572739604	-0.0925892716869	-0.194414032847	0.0896363884097	0.703123897675	0.458719287753	-0.163377763977	0.886305635345	0.191936250619	0.0581394791273	0.425846407829	-0.183025530854	0.617241842943	44.9360112011	12.5909382134	22.8171564325
18	0.0943974383033	0.0675065832207	0.10078370477	-0.000268004821317	-0.00500884311352	0.152221268804	-0.0784815477417	0.502744125878	-0.201364881168	0.487779338538	0.241272310187	0.45606056086	0.452261758228	-0.104810466026	-0.000233440514982	0.504945924372	-0.0693410526898	-0.00640533838031	0.379108087809	0.0377754902421	0.495134388958	33.5662684175	21.943222251	23.1355388079
19	0.490351110124	0.365920687391	-0.633216367148	0.780288775936	-0.77640732212	1.32911520502	0.869415244337	0.588284087152	0.246333892397	-0.224720821501	0.684943015153	0.533323718315	-2.07943544462	-0.465682442121	0.937238325857	0.239209236366	-0.452406970388	0.206666143145	-0.191276571574	-0.0490177083324	0.463583242754	37.5410836409	39.9804296724	26.0760572406
20	0.0680096372172	-0.0220568650943	0.125511423404	-0.00462425067307	0.0578446912762	0.146492777958	-0.0423399312676	-0.1290911664	-0.0107714948861	-0.829383046285	-0.144073687728	-0.19085008504	0.435975825085	-0.153149200894	-7.677469018E-5	0.461738404473	-0.0781884018291	0.000422322467638	0.305613527701	0.042856737912	0.499196734536	35.3841978153	25.1212350275	24.5443292764

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 162 through 171 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 172 through 199 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 200 through 218 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 219 through 224 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 225 through 234 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 79 through 103 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 104 through 122 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 123 through 144 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 145 through 154 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 155 through 171 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 172 through 193 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 194 through 228 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 229 through 235 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 79 through 91 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 92 through 102 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 103 through 122 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 123 through 135 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 136 through 144 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 145 through 154 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 155 through 161 )

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