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- PDB-7mwy: Structure of the drosophila STING cyclic dinucleotide binding domain -

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Basic information

Entry
Database: PDB / ID: 7mwy
TitleStructure of the drosophila STING cyclic dinucleotide binding domain
ComponentsSTING
KeywordsIMMUNE SYSTEM / STING / cyclic dinucleotide receptor
Function / homologyLysozyme - #40 / Lysozyme / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciesDrosophila eugracilis (fry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.84 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


Theoretical massNumber of molelcules
Total (without water)40,9011
Polymers40,9011
Non-polymers00
Water7,188399
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18330 Å2
Unit cell
Length a, b, c (Å)135.199, 135.199, 60.035
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein STING


Mass: 40901.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila eugracilis (fry) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O

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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: 3.87 Å3/Da / Density % sol: 68.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium citrate, 0.1 M Tris-HCl, 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: 1.84→44.91 Å / Num. obs: 54801 / % possible obs: 99.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 31.42 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.035 / Net I/σ(I): 11.2
Reflection shellResolution: 1.84→1.88 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3340 / CC1/2: 0.435 / Rpim(I) all: 0.656 / % possible all: 98.6

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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: 1.84→44.89 Å / SU ML: 0.2236 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.5355
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1937 2004 3.66 %
Rwork0.1795 52763 -
obs0.18 54767 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.32 Å2
Refinement stepCycle: LAST / Resolution: 1.84→44.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2845 0 0 399 3244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01382904
X-RAY DIFFRACTIONf_angle_d1.23033916
X-RAY DIFFRACTIONf_chiral_restr0.0805428
X-RAY DIFFRACTIONf_plane_restr0.01497
X-RAY DIFFRACTIONf_dihedral_angle_d13.14471087
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.890.31621410.32553689X-RAY DIFFRACTION98.46
1.89-1.940.3031420.26943755X-RAY DIFFRACTION99.26
1.94-1.990.27291400.23423743X-RAY DIFFRACTION99.85
1.99-2.060.24451410.213726X-RAY DIFFRACTION99.43
2.06-2.130.23781380.20163735X-RAY DIFFRACTION99.64
2.13-2.220.16931420.19193728X-RAY DIFFRACTION99.13
2.22-2.320.24881450.19193753X-RAY DIFFRACTION99.62
2.32-2.440.23141430.17973740X-RAY DIFFRACTION99.85
2.44-2.590.21051430.18323785X-RAY DIFFRACTION99.87
2.59-2.790.19911400.17463779X-RAY DIFFRACTION99.9
2.79-3.070.19541440.19113783X-RAY DIFFRACTION99.97
3.07-3.520.18151440.16993791X-RAY DIFFRACTION99.62
3.52-4.430.1461480.1533811X-RAY DIFFRACTION100
4.43-44.890.18181530.16573945X-RAY DIFFRACTION99.81
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)
10.2907995706370.0003058608423650.58230472550.483938328877-0.4385014941651.593344633170.01223072939220.06479303279060.00813222747407-0.00603981159074-0.041192971222-0.07226898231760.1633937083220.339843593096-0.05928722051250.151218149475-0.0212614147145-0.0006823345645530.313712544751-0.01292863332630.23479755717952.5324992166-52.763111607517.7177565487
21.134966816020.6874972241670.1041632276751.381388797910.467299209051.41306390845-0.2151546157290.3859305917880.123535378365-0.3755039930090.3130245112870.308762707329-0.1787774694280.1149251057740.1419668653480.320395474549-0.124396849528-0.048892987280.2718557021030.07170108502460.3112624513240.0568049683-37.9690851365-8.95866827716
30.8472580629130.657684474113-0.3363932330220.8083076281950.4492072388221.836898786130.0327829084406-0.1804081014720.361756930280.143795483521-0.05843875575270.239772664574-0.217852981022-0.193824155384-0.01907783289080.205584566527-0.01421708650210.008498607709930.2235715402450.01553803933140.32579720778830.7971876875-39.71245522884.89352587462
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -14 through 176 )-14 - 1761 - 191
22chain 'A' and (resid 177 through 252 )177 - 252192 - 267
33chain 'A' and (resid 253 through 337 )253 - 337268 - 352

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