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

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Basic information

Entry
Database: PDB / ID: 5cfm
TitleCrystal structure of anemone STING (Nematostella vectensis) in complex with 3', 3' cGAMP, c[G(3', 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 / autophagosome / positive regulation of type I interferon production / activation of innate immune response / 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 / Transmembrane protein 173 / 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 / Transmembrane protein 173 / 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-4BW / CITRATE ANION / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesNematostella vectensis (starlet sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.994 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)44,8827
Polymers43,4512
Non-polymers1,4315
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-17 kcal/mol
Surface area17310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.270, 81.270, 99.121
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-4BW / 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one / 3',3' cGAMP / c-GMP-AMP / c[G(3',5')pA(3',5')p]


Mass: 674.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O13P2
#3: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


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


Mass: 18.015 Da / Num. of mol.: 256 / 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: 4.35 Å3/Da / Density % sol: 71.72 %
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: 1.99→40.635 Å / Num. obs: 49839 / % possible obs: 99.5 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 13.4
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.739 / Mean I/σ(I) obs: 1.8 / % possible all: 93.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.994→40.635 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1902 1752 3.54 %Random selection
Rwork0.1699 ---
obs0.1706 49486 99.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.994→40.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3060 0 97 256 3413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083282
X-RAY DIFFRACTIONf_angle_d1.0534450
X-RAY DIFFRACTIONf_dihedral_angle_d14.7261222
X-RAY DIFFRACTIONf_chiral_restr0.046456
X-RAY DIFFRACTIONf_plane_restr0.005564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.994-2.04810.2841220.26713301X-RAY DIFFRACTION89
2.0481-2.10840.231340.22943709X-RAY DIFFRACTION100
2.1084-2.17640.21231290.22633709X-RAY DIFFRACTION100
2.1764-2.25420.28191400.21053739X-RAY DIFFRACTION100
2.2542-2.34440.19781250.19993681X-RAY DIFFRACTION100
2.3444-2.45110.21151340.19373691X-RAY DIFFRACTION100
2.4511-2.58030.20651360.23691X-RAY DIFFRACTION100
2.5803-2.7420.27431440.20553701X-RAY DIFFRACTION100
2.742-2.95360.21641330.20353701X-RAY DIFFRACTION100
2.9536-3.25080.20311420.18893733X-RAY DIFFRACTION100
3.2508-3.72090.16771420.1573665X-RAY DIFFRACTION100
3.7209-4.68680.17051260.12793710X-RAY DIFFRACTION100
4.6868-40.64340.14571450.14093703X-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)
10.55480.34080.28130.23790.32550.2244-0.11040.08050.3696-0.1252-0.00660.2514-0.5165-0.124-0.00050.4224-0.02490.01320.3566-0.01040.3852-28.59241.39660.5061
20.8871-0.33670.45913.16951.74470.9352-0.08790.0246-0.3699-0.15560.11580.0495-0.0040.0048-0.00010.35-0.06850.01980.3229-0.02890.3587-28.3264-16.6335-9.2988
30.9264-1.729-0.67333.02191.15390.8522-0.0535-0.2907-0.48650.47890.0776-0.20370.4018-0.21910.02880.3743-0.0972-0.0250.3103-0.0540.4404-29.8091-20.3807-6.2995
41.50790.0794-1.46852.21560.09090.88590.01610.03850.195-0.11770.03480.3551-0.1782-0.3959-0.00010.31880.005-0.0250.3980.02260.36-37.1494-1.74133.8574
50.8356-0.7364-0.01591.74861.09730.84560.04550.346-0.1552-0.4804-0.27620.4097-0.3704-0.4173-0.00030.446-0.0457-0.07070.4608-0.05340.3616-37.2018-12.7394-14.0601
60.53990.41790.26310.33350.03770.12780.0585-0.34220.4077-0.1110.00950.3817-0.2949-0.21010.00010.3437-0.00110.00750.39030.00780.3763-27.53892.00719.2032
72.6145-1.30041.89871.5767-0.65861.2161-0.0108-0.208-0.1694-0.01480.0506-0.3167-0.00490.01410.00050.2774-0.0259-0.01810.3920.01960.354-12.0537-7.241518.9961
81.6521-1.94180.99152.2306-1.2670.62430.15060.369-0.4432-0.4269-0.0935-0.40790.02060.50520.04990.2675-0.0201-0.05320.4464-0.00090.4518-8.0823-7.851916.0003
91.9892-0.4235-0.45541.4998-1.45631.00210.0014-0.14130.43050.06470.0132-0.0306-0.48040.0261-0.00010.3822-0.03190.01370.3367-0.03450.3646-20.55117.845.8363
100.7518-0.89710.7671.4819-0.54570.8517-0.3208-0.12420.24860.37610.0727-0.3714-0.4578-0.0857-0.00110.4187-0.0434-0.07420.476-0.02430.375-11.30533.734121.4921
110.00360.0090.06060.0468-0.06960.15040.6475-1.31820.66740.96280.25630.26920.3318-0.5513-0.0011.15590.234-0.10131.2384-0.02861.0269-9.5381-3.866134.8522
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 249 )
3X-RAY DIFFRACTION3chain 'A' and (resid 250 through 302 )
4X-RAY DIFFRACTION4chain 'A' and (resid 303 through 341 )
5X-RAY DIFFRACTION5chain 'A' and (resid 342 through 377 )
6X-RAY DIFFRACTION6chain 'B' and (resid 191 through 204 )
7X-RAY DIFFRACTION7chain 'B' and (resid 205 through 249 )
8X-RAY DIFFRACTION8chain 'B' and (resid 250 through 302 )
9X-RAY DIFFRACTION9chain 'B' and (resid 303 through 341 )
10X-RAY DIFFRACTION10chain 'B' and (resid 342 through 370 )
11X-RAY DIFFRACTION11chain 'B' and (resid 371 through 377 )

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