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- PDB-8hwj: Bacterial STING from Epilithonimonas lactis in complex with 3'3'-... -

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Basic information

Entry
Database: PDB / ID: 8hwj
TitleBacterial STING from Epilithonimonas lactis in complex with 3'3'-c-di-AMP
ComponentsCD-NTase-associated protein 12
KeywordsSIGNALING PROTEIN / CD-NTase-associated protein 12
Function / homology
Function and homology information


NAD+ glycohydrolase / NADP+ nucleosidase activity / defense response to virus / 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
Chem-2BA / CD-NTase-associated protein 12
Similarity search - Component
Biological speciesEpilithonimonas lactis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.553 Å
AuthorsWang, Y.-C. / Yang, C.-S. / Hou, M.-H. / Chen, Y.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)109-2311-B241-001 Taiwan
Ministry of Science and Technology (MoST, Taiwan)111-2311-B-039-001-MY3 Taiwan
CitationJournal: Nat Commun / Year: 2023
Title: Structural insights into the regulation, ligand recognition, and oligomerization of bacterial STING.
Authors: Hou, M.H. / Wang, Y.C. / Yang, C.S. / Liao, K.F. / Chang, J.W. / Shih, O. / Yeh, Y.Q. / Sriramoju, M.K. / Weng, T.W. / Jeng, U.S. / Hsu, S.D. / Chen, Y.
History
DepositionDec 30, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD-NTase-associated protein 12
B: CD-NTase-associated protein 12
C: CD-NTase-associated protein 12
D: CD-NTase-associated protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5716
Polymers75,2544
Non-polymers1,3172
Water3,099172
1
A: CD-NTase-associated protein 12
B: CD-NTase-associated protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2863
Polymers37,6272
Non-polymers6581
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-22 kcal/mol
Surface area16070 Å2
MethodPISA
2
C: CD-NTase-associated protein 12
D: CD-NTase-associated protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2863
Polymers37,6272
Non-polymers6581
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-24 kcal/mol
Surface area16550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.171, 52.713, 88.932
Angle α, β, γ (deg.)90.000, 114.883, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
CD-NTase-associated protein 12


Mass: 18813.592 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The GLY4 should be re-indexed as GLY151. / Source: (gene. exp.) Epilithonimonas lactis (bacteria) / Gene: IO89_10965 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A085BE66
#2: Chemical ChemComp-2BA / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate


Mass: 658.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O12P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.0, 0.1 M Sodium chloride, 30 % v/v PEG 3500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. obs: 20886 / % possible obs: 96.5 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 14.1
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1948

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
MOLREP11.7.03phasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.553→25.769 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / Cross valid method: THROUGHOUT / ESU R Free: 0.33
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2276 962 4.912 %
Rwork0.195 18622 -
all0.197 --
obs-19584 89.818 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 45.432 Å2
Baniso -1Baniso -2Baniso -3
1-0.439 Å20 Å20.571 Å2
2---0.735 Å2-0 Å2
3----0.164 Å2
Refinement stepCycle: LAST / Resolution: 2.553→25.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5151 0 88 172 5411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135337
X-RAY DIFFRACTIONr_bond_other_d0.0340.0175139
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.6497231
X-RAY DIFFRACTIONr_angle_other_deg2.2721.58311858
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5975636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.82924.323266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.75315983
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6621520
X-RAY DIFFRACTIONr_chiral_restr0.0790.2735
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025942
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021154
X-RAY DIFFRACTIONr_nbd_refined0.2090.21099
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2310.24810
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22544
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.22558
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2147
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1240.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2170.228
X-RAY DIFFRACTIONr_nbd_other0.2880.2106
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1460.26
X-RAY DIFFRACTIONr_mcbond_it3.9724.6532559
X-RAY DIFFRACTIONr_mcbond_other3.9724.6532558
X-RAY DIFFRACTIONr_mcangle_it6.5856.9653190
X-RAY DIFFRACTIONr_mcangle_other6.5846.9653191
X-RAY DIFFRACTIONr_scbond_it3.8814.9562778
X-RAY DIFFRACTIONr_scbond_other3.8784.9562775
X-RAY DIFFRACTIONr_scangle_it6.4557.2094041
X-RAY DIFFRACTIONr_scangle_other6.4527.2094040
X-RAY DIFFRACTIONr_lrange_it10.57753.5425824
X-RAY DIFFRACTIONr_lrange_other10.57853.5445824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.553-2.6190.27510.234869X-RAY DIFFRACTION57.7164
2.619-2.690.199470.2111001X-RAY DIFFRACTION68.5415
2.69-2.7670.283520.2271139X-RAY DIFFRACTION77.5896
2.767-2.8520.266580.241154X-RAY DIFFRACTION83.9335
2.852-2.9440.269600.2331258X-RAY DIFFRACTION92.1678
2.944-3.0470.277660.2321220X-RAY DIFFRACTION95.4006
3.047-3.160.204630.2251215X-RAY DIFFRACTION96.6717
3.16-3.2880.239670.2211164X-RAY DIFFRACTION94.1131
3.288-3.4320.241720.2121127X-RAY DIFFRACTION98.8458
3.432-3.5970.229550.21097X-RAY DIFFRACTION98.2097
3.597-3.7890.26580.1941049X-RAY DIFFRACTION98.5752
3.789-4.0150.214540.1781000X-RAY DIFFRACTION98.8743
4.015-4.2870.205450.158952X-RAY DIFFRACTION98.8107
4.287-4.6220.149430.153868X-RAY DIFFRACTION97.3291
4.622-5.0510.206310.152807X-RAY DIFFRACTION97.783
5.051-5.6280.263390.197722X-RAY DIFFRACTION96.9427
5.628-6.4610.291300.231677X-RAY DIFFRACTION99.2978
6.461-7.8220.204370.193558X-RAY DIFFRACTION99.3322
7.822-10.7050.169270.146461X-RAY DIFFRACTION98.9858
10.705-25.7690.33270.203284X-RAY DIFFRACTION93.5691

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