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- PDB-5cfl: Crystal structure of anemone STING (Nematostella vectensis) in co... -

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Basic information

Entry
Database: PDB / ID: 5cfl
TitleCrystal structure of anemone STING (Nematostella vectensis) in complex with 3', 3' c-di-GMP, c[G(3', 5')pG(3', 5')p]
ComponentsStimulator of Interferon Genes
KeywordsIMMUNE SYSTEM / STING / Cyclic-dinucleotide Binding Domain
Function / homology
Function and homology information


2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / reticulophagy / positive regulation of macroautophagy / autophagosome assembly / positive regulation of type I interferon production / activation of innate immune response / autophagosome / innate immune response / endoplasmic reticulum membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5200 / Stimulator of interferon genes protein / : / STING transmembrane domain / : / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / STING ligand-binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5200 / Stimulator of interferon genes protein / : / STING transmembrane domain / : / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / STING ligand-binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-C2E / CITRATE ANION / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesNematostella vectensis (starlet sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.836 Å
AuthorsKranzusch, P.J. / Wilson, S.C. / Lee, A.S.Y. / Berger, J.M. / Doudna, J.A. / Vance, R.E.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI063302 United States
CitationJournal: Mol.Cell / Year: 2015
Title: Ancient Origin of cGAS-STING Reveals Mechanism of Universal 2',3' cGAMP Signaling.
Authors: Kranzusch, P.J. / Wilson, S.C. / Lee, A.S. / Berger, J.M. / Doudna, J.A. / Vance, R.E.
History
DepositionJul 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Sep 30, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stimulator of Interferon Genes
B: Stimulator of Interferon Genes
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8987
Polymers43,4512
Non-polymers1,4475
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-10 kcal/mol
Surface area16800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.109, 81.109, 97.067
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Stimulator of Interferon Genes / Predicted protein


Mass: 21725.723 Da / Num. of mol.: 2 / Fragment: UNP residues 193-377
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nematostella vectensis (starlet sea anemone)
Gene: v1g246111 / Production host: Escherichia coli (E. coli) / References: UniProt: A7SLZ2
#2: 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
#3: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.24 Å3/Da / Density % sol: 71.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.8 M ammonium citrate pH 7.0

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.836→48.54 Å / Num. obs: 61587 / % possible obs: 98.7 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 10.3
Reflection shellResolution: 1.836→1.9 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 1.5 / % possible all: 82.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.836→40.555 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2087 1606 2.62 %Random Selection
Rwork0.1721 ---
obs0.1729 61202 98.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.836→40.555 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3060 0 98 392 3550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033232
X-RAY DIFFRACTIONf_angle_d0.7364372
X-RAY DIFFRACTIONf_dihedral_angle_d15.4581218
X-RAY DIFFRACTIONf_chiral_restr0.029448
X-RAY DIFFRACTIONf_plane_restr0.004562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8363-1.89560.32921300.30494466X-RAY DIFFRACTION81
1.8956-1.96330.26981480.25185483X-RAY DIFFRACTION100
1.9633-2.04190.23981520.21155532X-RAY DIFFRACTION100
2.0419-2.13480.21281440.19535490X-RAY DIFFRACTION100
2.1348-2.24740.23381530.18985551X-RAY DIFFRACTION100
2.2474-2.38820.23851440.19345515X-RAY DIFFRACTION100
2.3882-2.57250.19441500.19495472X-RAY DIFFRACTION100
2.5725-2.83140.25931500.20165509X-RAY DIFFRACTION100
2.8314-3.24090.20671520.18115551X-RAY DIFFRACTION100
3.2409-4.08260.18171380.1455529X-RAY DIFFRACTION100
4.0826-40.56440.18041450.13715498X-RAY DIFFRACTION100
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)
10.6853-0.4635-0.10280.4280.39640.37320.1086-0.0419-0.3414-0.076-0.03910.23020.277-0.43050.00020.2534-0.0226-0.02870.31980.03680.304112.805921.1836-11.1701
20.68630.20260.00480.2572-0.08270.02060.15680.49220.5181-0.13670.26340.2146-0.1464-0.487-0.00040.23050.04380.03190.3330.08110.306720.905935.2834-22.7787
31.91350.597-0.54791.2704-0.63250.2929-0.00990.02690.02-0.0259-0.1003-0.31210.09930.17780.00040.25040.04630.01330.31590.00930.272532.126727.9107-20.1107
40.47330.8241-0.77261.0129-0.94131.86220.0439-0.10140.21030.1209-0.0448-0.2544-0.07480.3307-0.00160.22980.02360.01820.35770.02620.385333.27330.7396-16.0049
50.41470.2366-0.06330.8499-1.06840.88960.01250.0520.2227-0.0375-0.0889-0.29020.15750.2969-0.04740.21680.04410.05990.34770.02790.344131.475531.1758-19.4163
61.9649-0.0417-0.05211.0507-0.33820.4005-0.00090.0385-0.4286-0.00010.04810.07320.3258-0.04830.00010.31510.0132-0.0230.238-0.01730.319519.879515.3128-8.0792
71.04130.7563-0.79830.661-0.0491.25140.04130.2702-0.1773-0.413-0.0806-0.10290.52320.017100.37280.0523-0.00250.3901-0.03650.25925.017420.1043-22.4176
80.47060.5951-0.57511.3889-0.84020.7104-0.30450.5235-0.2854-0.90650.2178-0.22621.02030.0171-0.02210.49850.0650.11450.5045-0.0130.366133.511521.9042-30.197
90.963-0.6573-0.5140.34260.09730.6279-0.004-0.0073-0.26970.06420.06210.12140.30180.03290.00020.27870.0222-0.04690.2393-0.00340.284312.681222.8964-2.0071
100.08410.0840.09120.616-0.04920.25770.1528-0.38070.01890.80280.3242-0.96020.48670.36330.00990.28880.0811-0.0440.3198-0.0880.349320.407736.33310.283
110.89-0.05040.25332.19740.61590.0926-0.0527-0.04590.29160.0299-0.02890.1545-0.0842-0.1350.00090.26270.0509-0.00030.3146-0.01680.27618.11241.77316.5259
120.37180.66930.34041.10160.91841.7956-0.02150.14260.4125-0.15670.0196-0.0928-0.3214-0.1623-0.00910.30440.0857-0.0250.2848-0.04780.38959.983544.17292.4215
130.65640.40651.02680.60.65771.0282-0.089-0.10760.36360.00960.0026-0.0645-0.1878-0.2675-0.07650.27940.07850.01160.2805-0.05170.329111.257542.83645.8382
141.6669-0.15760.35951.71910.43520.60270.05320.0139-0.30920.0540.03360.32240.2152-0.258100.2395-0.0288-0.00520.29040.03260.30673.303324.8337-5.5296
150.25140.094-0.3171.24410.89081.26790.0433-0.4061-0.08630.1818-0.03090.2490.3268-0.4056-0.00020.32610.03330.02370.41340.02650.25994.904731.7138.8169
160.60730.32120.43561.07180.70511.2450.2551-0.68320.0080.7079-0.33130.36840.5813-0.9113-0.02010.42940.02160.06760.5523-0.08540.36042.205939.94516.5789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 191 through 204 )
2X-RAY DIFFRACTION2chain 'A' and (resid 205 through 220 )
3X-RAY DIFFRACTION3chain 'A' and (resid 221 through 249 )
4X-RAY DIFFRACTION4chain 'A' and (resid 250 through 272 )
5X-RAY DIFFRACTION5chain 'A' and (resid 273 through 302 )
6X-RAY DIFFRACTION6chain 'A' and (resid 303 through 341 )
7X-RAY DIFFRACTION7chain 'A' and (resid 342 through 359 )
8X-RAY DIFFRACTION8chain 'A' and (resid 360 through 377 )
9X-RAY DIFFRACTION9chain 'B' and (resid 191 through 206 )
10X-RAY DIFFRACTION10chain 'B' and (resid 207 through 220 )
11X-RAY DIFFRACTION11chain 'B' and (resid 221 through 249 )
12X-RAY DIFFRACTION12chain 'B' and (resid 250 through 272 )
13X-RAY DIFFRACTION13chain 'B' and (resid 273 through 302 )
14X-RAY DIFFRACTION14chain 'B' and (resid 303 through 341 )
15X-RAY DIFFRACTION15chain 'B' and (resid 342 through 359 )
16X-RAY DIFFRACTION16chain 'B' and (resid 360 through 377 )

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