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- PDB-7mwz: Structure of drosophila STING in complex with 3'2'-cGAMP -

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Basic information

Entry
Database: PDB / ID: 7mwz
TitleStructure of drosophila STING in complex with 3'2'-cGAMP
ComponentsSTING
KeywordsIMMUNE SYSTEM / STING / cyclic dinucleotide receptor
Function / homologyStimulator of interferon genes protein / Lysozyme - #40 / Lysozyme / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta / 3'2'-cGAMP
Function and homology information
Biological speciesDrosophila eugracilis (fry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsSlavik, K.M. / Ragucci, A.E. / Kranzusch, P.J.
CitationJournal: Nature / Year: 2021
Title: cGAS-like receptors sense RNA and control 3'2'-cGAMP signalling in Drosophila.
Authors: Slavik, K.M. / Morehouse, B.R. / Ragucci, A.E. / Zhou, W. / Ai, X. / Chen, Y. / Li, L. / Wei, Z. / Bahre, H. / Konig, M. / Seifert, R. / Lee, A.S.Y. / Cai, H. / Imler, J.L. / Kranzusch, P.J.
History
DepositionMay 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 15, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STING
B: STING
C: STING
D: STING
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,9536
Polymers163,6044
Non-polymers1,3492
Water9,206511
1
A: STING
B: STING
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4773
Polymers81,8022
Non-polymers6741
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-17 kcal/mol
Surface area32610 Å2
MethodPISA
2
C: STING
D: STING
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4773
Polymers81,8022
Non-polymers6741
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-20 kcal/mol
Surface area31130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.923, 95.046, 140.138
Angle α, β, γ (deg.)90.000, 93.934, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
STING


Mass: 40901.070 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila eugracilis (fry) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-4UR / 3'2'-cGAMP / 2-amino-9-[(2S,5R,7R,8R,10R,12aR,14R,15R,15aS,16R)-7-(6-amino-9H-purin-9-yl)-2,10,15,16-tetrahydroxy-2,10-dioxidooctahydro-12H-5,8-methanofuro[3,2-l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecin-14-yl]-1,9-dihydro-6H-purin-6-one


Mass: 674.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1-0.2 M sodium acetate pH 4.8, 0.2 M ammonium formate, 20-22% PEG-3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→48.84 Å / Num. obs: 89677 / % possible obs: 99.7 % / Redundancy: 7.1 % / Biso Wilson estimate: 42.5 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.032 / Net I/σ(I): 10.7
Reflection shellResolution: 2→2.04 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4600 / CC1/2: 0.561 / Rpim(I) all: 0.759 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: SAD-phased model of the selenomethionine derivative

Resolution: 2→48.84 Å / SU ML: 0.3635 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.0548
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.283 2004 2.24 %
Rwork0.2472 87540 -
obs0.2479 89544 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.01 Å2
Refinement stepCycle: LAST / Resolution: 2→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10943 0 90 511 11544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001811262
X-RAY DIFFRACTIONf_angle_d0.435615194
X-RAY DIFFRACTIONf_chiral_restr0.03741666
X-RAY DIFFRACTIONf_plane_restr0.00311905
X-RAY DIFFRACTIONf_dihedral_angle_d12.71814178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.40931460.38416162X-RAY DIFFRACTION98.44
2.05-2.110.42081430.35626211X-RAY DIFFRACTION99.58
2.11-2.170.35921480.34216219X-RAY DIFFRACTION99.78
2.17-2.240.33211280.31646287X-RAY DIFFRACTION99.74
2.24-2.320.35481540.31386243X-RAY DIFFRACTION99.46
2.32-2.410.35131340.31016199X-RAY DIFFRACTION99.29
2.41-2.520.31681500.30716176X-RAY DIFFRACTION98.92
2.52-2.650.36581410.30666250X-RAY DIFFRACTION99.81
2.65-2.820.33441390.29136276X-RAY DIFFRACTION99.69
2.82-3.040.3191400.27366277X-RAY DIFFRACTION99.92
3.04-3.340.30381520.26186248X-RAY DIFFRACTION99.74
3.34-3.830.2531450.2246271X-RAY DIFFRACTION99.44
3.83-4.820.22981390.19966315X-RAY DIFFRACTION99.97
4.82-48.840.24151450.20446406X-RAY DIFFRACTION99.53
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)
1-0.0351926246888-0.30832303588-0.009694879826252.227238388670.8273724697834.56216884983-0.06706991088270.0128181378556-0.267097846010.188827726532-0.2392312033920.540483343027-0.359857783561-0.860213689040.1738494114770.4079754543440.0005423739290550.01010098151190.584186275672-0.0449932383120.683377439251-34.65949271942.2215318186718.8005057265
22.391172983470.2546277102051.080196252753.09251423764-0.7293351811462.061889008730.141063824478-0.28493358468-0.121317047310.070097375864-0.0111894500420.2841076950040.102912229862-0.256735724905-0.1501415416470.2210185496440.03395137153480.04352771601720.306469160146-0.02142072414010.311304940665-37.6614436927-17.4709007236-15.1446761618
35.11591915809-0.914888876728-0.6226460680135.705124558450.7888433970317.552735830380.07704209462720.5793138912420.4686378805390.567666177797-0.01402583251550.9530772652310.0561933029877-0.690634026052-0.01647648909430.376568517204-0.0655131617680.03924349113970.4557169703880.006038129224390.673146801444-29.6491495082-25.289883917222.8774483713
44.54472589161.70559307665-2.912060264312.717885586750.7458054686625.86214519976-0.1986835712680.09460021540730.1484497989290.387472607996-0.0725286574587-0.468027891621.085020553561.297609769020.1703335128850.7540080241810.1745579445640.07359374483210.8839260885250.2407867903530.825390543446-8.77962488775-22.704547977217.7815033125
52.302520511890.204535798963-1.005204504012.033228244120.05264555789482.008002664560.0672265176893-0.2049247193690.04374586552950.155058304498-0.0881724898096-0.317551215764-0.1472112311290.05826301545080.03586920945110.2565944393930.0255601622872-0.02765033868530.304342424187-0.01637850044850.390018619179-14.3861731884-2.70423851265-13.0721006585
66.95387713178-0.303611197223-3.284030238176.92779888749-0.1077027665797.2978526164-0.077529246322-0.3205155336690.632939869582-0.4776686328870.451253576992-0.971696537060.3844477199160.784784270926-0.212752495850.40207125417-0.00690743244025-0.002412629759790.375028699440.03719370147520.5219309540140.645716730816-14.948402876145.4655156512
73.11403684582-2.3895342326-1.533369990284.792919800421.970329987855.905282364330.2896594298510.9671938361520.589814441903-1.20590197037-0.6044493330520.659436609193-0.346475500212-1.171621922160.3186650833160.9576800787140.124628840507-0.1510287115320.7157813899-0.007194254988261.00591659495-18.1013068895-7.5941150968244.6881042279
8-0.04341054443650.0552983779658-0.7583091483191.146005582270.7526088197148.91719100779-0.02033375085430.120331703799-0.288120972923-0.00361317367075-0.09238593361650.4702834731550.529047996984-0.9704091002850.1244414989840.702080446385-0.07523494390850.02908376436890.65603551376-0.08098193336540.890861502109-19.278209561-7.4078403113766.3040041765
92.04028947228-1.160245772170.03243978393433.35674952441-0.1955664111711.83389307023-0.02805974880530.291879268528-0.0482285972349-0.3291487650830.09251347916640.1580960456420.141216004031-0.124807957725-0.03346483087720.539376032203-0.149931354903-0.03788007281060.396878185241-0.06655500673740.286191191348-16.819117176611.05065002483.6715165117
100.293935040649-0.1711744990361.026861617943.22316952303-2.943042661754.224873849250.1598581553220.1121463834550.243351344929-0.678599079044-0.2199541261340.1138089513440.4779985534060.3749153996910.007232730676460.863348460359-0.0165665692705-0.1139001088650.6196759579470.01639476290170.6869935757421.5489919338513.210872345655.6844400735
111.68425758190.1476803528360.3335817941123.010628445731.256920764032.93607049470.1304622088290.152341723889-0.208041413878-0.1676926059250.1861190986-0.716749464377-0.02895365364930.528542037824-0.3159446381770.572330334745-0.100159294434-0.01026289203180.521337529874-0.1979183301650.6437193454456.50732615975-7.1857688275683.9122737243
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -14 through 162 )AA-14 - 1621 - 177
22chain 'A' and (resid 163 through 337 )AA163 - 337178 - 351
33chain 'B' and (resid -14 through 45 )BC-14 - 451 - 60
44chain 'B' and (resid 46 through 141 )BC46 - 14161 - 156
55chain 'B' and (resid 142 through 337 )BC142 - 337157 - 352
66chain 'C' and (resid -13 through 45 )CD-13 - 451 - 59
77chain 'C' and (resid 46 through 108 )CD46 - 10860 - 122
88chain 'C' and (resid 109 through 176 )CD109 - 176123 - 188
99chain 'C' and (resid 177 through 337 )CD177 - 337189 - 349
1010chain 'D' and (resid -13 through 176 )DF-13 - 1761 - 144
1111chain 'D' and (resid 177 through 333 )DF177 - 333145 - 301

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