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

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7ebd
TitleBacterial STING in complex with c-di-GMP
ComponentsTIR-like domain-containing protein
KeywordsSIGNALING PROTEIN / second messenger / complex / cyclic dinucleotide / antiviral pathway
Function / homology
Function and homology information


NAD+ glycohydrolase / NADP+ nucleosidase activity / nucleotide binding
Similarity search - Function
CD-NTase-associated protein 12/Pycsar effector protein, TIR domain / CAP12/Pycsar effector protein, TIR domain / Prokaryotic STING domain / Prokaryotic STING domain
Similarity search - Domain/homology
ACETATE ION / Chem-C2E / CD-NTase-associated protein 12
Similarity search - Component
Biological speciesPrevotella corporis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsKo, T.-P. / Wang, Y.-C. / Yang, C.-S. / Hou, M.-H. / Chen, Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: 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
DepositionMar 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: 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
Revision 1.2Oct 16, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TIR-like domain-containing protein
B: TIR-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0715
Polymers37,2622
Non-polymers8083
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-12 kcal/mol
Surface area15230 Å2
MethodPISA
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 number18
Space group name H-MP21212
Space group name HallP22ab
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
IDModelComponents
11B-624-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLUGLUchain 'A'AA157 - 1824 - 29
12PROPROLYSLYSchain 'A'AA184 - 20131 - 48
13PROPROSERSERchain 'A'AA203 - 21350 - 60
14LEULEUGLNGLNchain 'A'AA216 - 22763 - 74
15SERSERASPASPchain 'A'AA229 - 25276 - 99
16PROPROASPASPchain 'A'AA254 - 265101 - 112
17TYRTYRGLUGLUchain 'A'AA267 - 286114 - 133
18ASNASNGLNGLNchain 'A'AA288 - 313135 - 160
29GLYGLYGLUGLUchain 'B'BB157 - 1824 - 29
210PROPROLYSLYSchain 'B'BB184 - 20131 - 48
211PROPROSERSERchain 'B'BB203 - 21350 - 60
212LEULEUGLNGLNchain 'B'BB216 - 22763 - 74
213SERSERASPASPchain 'B'BB229 - 25276 - 99
214PROPROASPASPchain 'B'BB254 - 265101 - 112
215TYRTYRGLUGLUchain 'B'BB267 - 286114 - 133
216ASNASNGLNGLNchain 'B'BB288 - 313135 - 160

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Components

#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


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


Mass: 690.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.83 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.97836 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97836 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 14459 / % possible obs: 99.8 % / Redundancy: 9.3 % / Biso Wilson estimate: 27.66 Å2 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.036 / Net I/σ(I): 22.6
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 9 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1410 / Rpim(I) all: 0.215 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PHENIXphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2487 720 4.92 %
Rwork0.1883 25305 -
obs0.1911 14413 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.08 Å2
Refinement stepCycle: LAST / Resolution: 2.25→21.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2532 0 54 262 2848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212634
X-RAY DIFFRACTIONf_angle_d0.54933564
X-RAY DIFFRACTIONf_chiral_restr0.0402404
X-RAY DIFFRACTIONf_plane_restr0.0028446
X-RAY DIFFRACTIONf_dihedral_angle_d16.83381576
LS refinement shellResolution: 2.25→2.34 Å
RfactorNum. reflection% reflection
Rfree0.3026 144 -
Rwork0.2748 1385 -
obs--98.37 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.462067574411-0.1078321137920.2869039138690.1123297731450.03068155693320.315527653392-0.08984289244790.254234977108-0.0688491428499-0.0275280556975-0.08815631988450.1340924108610.0259713578440.164722225639-0.21878626620.11023644582-0.02071681227830.03283873350710.075120940662-0.002426509432720.11690910669331.493729825520.8752778934-7.7942712153
20.0127148192133-0.01720537784020.002379884605150.108078625856-0.07190897910860.0467402298834-0.05950005624390.01406049807930.12140515488-0.0804208613585-0.0545545018725-0.0108393550528-0.00691908301325-0.227120671076-0.01523197009480.4490248595210.052078437319-0.0524357844680.2168220615220.08453404362010.4139742751439.179716825540.7356327994-10.2954181504
30.0391622725649-0.006149853578760.008946114683270.06073128923840.055260817850.03064826963220.0464615866829-0.1073653767490.1027591231470.0532424874825-0.00899270541354-0.1352746986220.03783323898910.03609376064450.0001968729365530.126175883982-0.0224092847844-0.008234531352220.1790252405320.01460109436710.15300345629739.66861413721.27585226573.34221429082
40.0576869958817-0.0627777596129-0.008661110822170.06764197702440.02519088334690.149892270222-0.179946653656-0.00349233633268-0.004380714007430.170574563494-0.06505873386990.0239679379217-0.145027236646-0.0705308549974-0.1740410918130.471316543533-0.0524448469081-0.02827428832540.1803614928020.001104158888360.06856526585137.696287256126.91247391510.4863307906
50.01473372548450.00826596235536-0.008637570563580.0154280768062-0.01418744740380.005129563804890.1230100031490.0191799669194-0.0602070987088-0.0926679393088-0.0157724966554-0.0906682325362-0.1193444990930.00488921952097-1.14451630041E-50.199512143675-0.00107956332489-0.01109326148070.23225947294-0.01610431219540.36651028220237.095631247234.98677364950.79270686221
60.0905686074817-0.04254025057760.0223342007110.1124855989450.2083807298890.403721272876-0.0841053120131-0.2037736837680.2077997996250.115175919091-0.00398989713710.0247452011125-0.318417544379-0.239032640222-0.04564446158990.146526109667-0.012093690784-0.03333814220680.1035278336810.03228628389570.20828638879935.502238513831.9530054162-3.89233716784
70.001749298491190.004366549037160.002405616460850.00530158544417-0.004063076551880.0143504195639-0.0503141896367-0.144970231856-0.001416853133990.0129006744260.0615315083272-0.0428982693983-0.0176817235296-0.0206840278112-0.008415044256240.08858148406220.0394682197199-0.01348850481950.1603268338520.0707013306840.12989042812728.550482039911.069768148.95619172579
8-0.0004414830596820.001415771761240.0006202469590445.0276419923E-5-0.001915388910150.000981465889411-0.034633978735-0.08390361913910.05808947270890.0161600739909-0.0197696300442-0.02143677548160.0381911498380.04254741776932.16009819196E-50.897277810199-0.00179146252062-0.06182340294960.7540130380550.1939454642270.41501278829932.97858714214.5655478005918.7451247052
90.03554384657050.006316575206610.02008486416480.0830551131630.02731319317570.0315688893125-0.0485613349343-0.309973038666-0.1226747642940.2489344096420.120458727899-0.2121679032670.1816986948180.206940107470.07108664696740.1388588765060.2318636151710.279499200552-0.012650772553-0.2140868736530.0064025050128337.82473674069.269613213090.375111665205
100.142351073530.02386036851730.04760978017830.09110952055660.03166617859680.0818435968124-0.02650218891660.0727210971201-0.164294925893-0.2939420493690.210560395889-0.128657644313-0.04857869928740.07963654996110.200343761775-0.0763212769177-0.1209592893360.2339524054020.1506390156140.104765106779-0.055815966998541.963868683821.097633581-9.4408234396
110.186241382492-0.04375500504470.1165278669260.036557029273-0.07224486811010.206909933572-0.100371336635-0.120058058801-0.05389663415650.06012448929070.0531290089507-0.0696838619752-0.000835103049269-0.0157421324715-0.06953197653160.140216607121-0.01349959037040.01559961423930.1206454956940.0009067858866040.13403580215919.430651214120.60020134337.59686488624
120.007983585483450.0149584341383-0.02205891383850.103137484459-0.09357304758160.15245638438-0.149578482548-0.0223193848081-0.0725221754209-0.0601499671388-0.1420468842840.0908063213402-0.2359621411360.15767682238-0.006804038437410.576909685833-0.0427780220975-0.0446186880380.275794262542-0.1646053336750.44691797849511.129591049639.99709862289.90747829688
130.0213837632772-0.004087694394810.02143987071470.0119893541946-0.01367390522040.1618386081010.01621074078030.0037194376221-0.0360670654165-0.159777967159-0.2024687141460.08038178456170.1621718105260.12848541212-0.006845028580210.1892527419190.00602043901981-0.003883625603940.142548332248-0.02016201346990.11257616900911.152781367220.5722220562-3.4501889463
140.03946067583780.0332984670805-0.01594531094640.032412120122-0.01695190709250.0105316616884-0.1443854591390.174852010705-0.0202455519709-0.218095976362-0.066113156625-0.0298068932972-0.05108743469150.133271313013-0.02724211344250.3624341287330.0338384793261-0.0538208884090.361651088090.01754435156170.10320852168512.79352498426.3001203127-10.5912417794
150.02181186649250.000747565695882-0.01471205906590.01625702721580.01737730759180.01200304029710.0606250206018-0.106020352447-0.04392506493490.130140546987-0.1129558261410.141309555771-0.1543134845890.005145181290870.0001228680996410.243079897132-0.022251881243-0.03495383093040.2346153552010.02886714980280.38083367295913.139594458134.3278847855-0.997079036609
160.06067899535320.0833013496136-0.06391609984210.102797221978-0.0819274293340.0482676322180.1118805848740.07505808664510.3202454099590.0214253216065-0.0170371470206-0.185065084725-0.1713535569750.2104484659570.005377405808290.14270160594-0.0496333874116-0.003607204296720.195367233265-0.02470588042710.20025466355814.870481907631.47282218243.72353500774
170.0248623010981-0.0180835343755-0.03371634792320.00652707405650.01834269223710.0443877516748-0.05419511581530.217774526765-0.0958418521701-0.0802689223412-0.002873109500180.01752017653920.0285957335916-0.0369940780081-0.05479416163850.0875199087982-0.122227939079-0.04643694822910.122562013845-0.2364144594870.044355308865122.72284961712.0766927336-8.81966788797
180.00247227774407-0.00362830002616-0.001097580143930.0009576904287010.00161770706646-0.000617744830543-0.02499015137950.0111426153465-0.00304759184891-0.0437572492208-0.000701231371171-0.06740470499190.0576693716886-0.0009102338326431.98878961656E-51.373252106760.325369914426-0.04541564528861.345310765930.2325131368281.2638148394119.44309250083.49888505031-17.5562831852
190.0465641753899-0.004875271441380.04514827014170.0318407151822-0.007622539898930.0544847963833-0.1033642003410.355607121844-0.316830188744-0.103813064462-0.004256490876040.223623114070.0433006380906-0.1368036312150.0009160065373590.153678200871-0.1145419859270.05738005794670.0507459107869-0.02738695669440.29602879575813.54893498938.620842375-0.741849643524
200.0205443051187-0.0154539928878-0.01798336437660.285088393812-0.02783894769360.0327239397794-0.133463762539-0.0225748125009-0.07625470592250.279191425056-0.01020864286350.0716371174072-0.0340719292092-0.0751786329180.00995954498640.05072875672540.01281903362180.0946881360160.192212189309-0.0657918707809-0.2081672227678.8124719800220.30673256539.33338323278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 157 through 181 )
2X-RAY DIFFRACTION2chain 'A' and (resid 182 through 194 )
3X-RAY DIFFRACTION3chain 'A' and (resid 195 through 209 )
4X-RAY DIFFRACTION4chain 'A' and (resid 210 through 220 )
5X-RAY DIFFRACTION5chain 'A' and (resid 221 through 228 )
6X-RAY DIFFRACTION6chain 'A' and (resid 229 through 254 )
7X-RAY DIFFRACTION7chain 'A' and (resid 255 through 267 )
8X-RAY DIFFRACTION8chain 'A' and (resid 268 through 276 )
9X-RAY DIFFRACTION9chain 'A' and (resid 277 through 299 )
10X-RAY DIFFRACTION10chain 'A' and (resid 300 through 314 )
11X-RAY DIFFRACTION11chain 'B' and (resid 157 through 181 )
12X-RAY DIFFRACTION12chain 'B' and (resid 182 through 194 )
13X-RAY DIFFRACTION13chain 'B' and (resid 195 through 209 )
14X-RAY DIFFRACTION14chain 'B' and (resid 210 through 220 )
15X-RAY DIFFRACTION15chain 'B' and (resid 221 through 228 )
16X-RAY DIFFRACTION16chain 'B' and (resid 229 through 254 )
17X-RAY DIFFRACTION17chain 'B' and (resid 255 through 266 )
18X-RAY DIFFRACTION18chain 'B' and (resid 267 through 276 )
19X-RAY DIFFRACTION19chain 'B' and (resid 277 through 299 )
20X-RAY DIFFRACTION20chain 'B' and (resid 300 through 314 )

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