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

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Basic information

Entry
Database: PDB / ID: 5cfq
TitleCrystal structure of anemone STING (Nematostella vectensis) in complex with 2',3' cGAMP, c[G(2',5')pA(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 / : / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5200 / Stimulator of interferon genes protein / : / 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
cGAMP / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesNematostella vectensis (starlet sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.099 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)44,3185
Polymers43,4512
Non-polymers8673
Water1,00956
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-42 kcal/mol
Surface area15760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.497, 77.971, 101.347
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-1SY / cGAMP / 2',3' cGAMP / c-GMP-AMP / c[G(2',5')pA(3',5')p]


Mass: 674.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O13P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 1.84 Å3/Da / Density % sol: 33.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 500 mM LiSO4, 2% PEG-8000 / PH range: 4.0 - 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: Feb 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.099→42.49 Å / Num. obs: 19434 / % possible obs: 99.6 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.024 / Net I/σ(I): 16.2
Reflection shellResolution: 2.099→2.16 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 1.6 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.099→38.985 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 968 5.01 %Random selection
Rwork0.2423 ---
obs0.2432 19337 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.099→38.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2963 0 55 56 3074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033145
X-RAY DIFFRACTIONf_angle_d0.7334264
X-RAY DIFFRACTIONf_dihedral_angle_d15.0851166
X-RAY DIFFRACTIONf_chiral_restr0.03443
X-RAY DIFFRACTIONf_plane_restr0.004532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.099-2.20930.34911320.34492499X-RAY DIFFRACTION97
2.2093-2.34770.38571350.38592567X-RAY DIFFRACTION99
2.3477-2.5290.35991370.32282611X-RAY DIFFRACTION100
2.529-2.78340.37041380.30442604X-RAY DIFFRACTION100
2.7834-3.1860.3231370.2942621X-RAY DIFFRACTION100
3.186-4.01340.25941410.22582675X-RAY DIFFRACTION100
4.0134-38.99210.18451480.18562792X-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)
11.8985-1.56660.43921.9728-0.684-0.1754-0.1612-0.09220.2114-0.62550.27920.2542-0.4870.1181-0.05750.5394-0.171-0.03570.40320.00470.28712.291589.1596112.195
21.1292-1.1288-2.46644.18093.39654.29020.3781-0.7934-0.05661.7329-0.86010.0230.09741.7394-0.29710.9029-0.4469-0.0831.02880.04330.774829.696687.3511118.5342
31.31380.6451.24395.3403-2.94382.6847-0.16280.64970.37320.93410.74360.7743-2.0141-0.21830.52111.4505-0.0460.19340.579-0.02170.57146.494293.8791122.9559
40.7038-0.3789-0.191-0.18480.03851.27920.6303-0.11610.21050.1885-0.4884-0.1261-0.29380.63050.11450.8692-0.30330.060.5310.03860.457122.150194.1862112.8312
50.7282-0.93350.20243.4085-1.53410.7518-0.0890.3546-0.2476-0.2848-0.2923-0.26870.34910.6429-0.00290.2968-0.00470.03590.61640.02890.537118.697670.5068118.8593
60.67180.0549-1.83282.5809-0.17791.42180.00810.6922-0.2212-0.25950.0275-0.36140.4020.1262-0.00050.8935-0.0716-0.02410.63560.04370.587721.985784.6661105.8347
71.66151.1289-0.37980.8790.77694.35520.2684-0.1503-0.29210.048-0.1224-0.4607-0.89790.42080.15680.3287-0.0539-0.01150.42210.02790.396512.593179.9708134.7459
80.69260.00670.28330.25740.00740.0896-0.0107-1.37030.78460.13410.36070.4647-0.5270.21570.0011.17510.01070.09450.8778-0.1140.8313.651593.618147.1588
92.54791.08680.42450.79590.20151.57220.9897-0.0715-0.2387-1.613-0.6310.15470.3217-1.02090.25461.16710.2505-0.06240.5891-0.0410.6522-7.005983.0514133.4683
101.5189-1.1241-0.40031.74862.41619.0244-0.0675-0.2776-0.15560.91990.19791.0459-2.2433.6572-0.08161.4659-0.40630.3837-0.02280.05770.721813.646292.6515130.5414
112.125-0.04880.0536-0.65710.34260.84270.4022-0.11840.44880.1504-0.06680.2627-0.9828-0.48720.00940.95590.13570.26640.36980.03010.5902-1.491888.6683140.3253
123.83740.7726-1.20562.9543-0.70371.6627-0.08250.0349-0.3688-0.11370.04190.49450.5571-0.351-0.00150.2812-0.0254-0.0130.32650.02070.58022.315669.3168125.9169
130.53240.2335-1.17053.18290.82641.81380.1607-0.6483-0.4190.0164-0.21150.3541-0.02990.05580.00010.6208-0.005-0.02420.480.10510.4842-1.190677.3432142.8446
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 193 through 239 )
2X-RAY DIFFRACTION2chain 'A' and (resid 240 through 261 )
3X-RAY DIFFRACTION3chain 'A' and (resid 262 through 277 )
4X-RAY DIFFRACTION4chain 'A' and (resid 278 through 302 )
5X-RAY DIFFRACTION5chain 'A' and (resid 303 through 340 )
6X-RAY DIFFRACTION6chain 'A' and (resid 341 through 372 )
7X-RAY DIFFRACTION7chain 'B' and (resid 193 through 219 )
8X-RAY DIFFRACTION8chain 'B' and (resid 220 through 233 )
9X-RAY DIFFRACTION9chain 'B' and (resid 234 through 261 )
10X-RAY DIFFRACTION10chain 'B' and (resid 262 through 277 )
11X-RAY DIFFRACTION11chain 'B' and (resid 278 through 302 )
12X-RAY DIFFRACTION12chain 'B' and (resid 303 through 341 )
13X-RAY DIFFRACTION13chain 'B' and (resid 342 through 371 )

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