+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26617 | ||||||||||||||||||||||||||||||||||||
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Title | SfSTING with c-di-GMP double fiber | ||||||||||||||||||||||||||||||||||||
Map data | SfSTING with c-di-GMP double fiber sharpened map | ||||||||||||||||||||||||||||||||||||
Sample |
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Keywords | STING / bacterial / filament / ANTIVIRAL PROTEIN | ||||||||||||||||||||||||||||||||||||
Function / homology | Function and homology information NAD+ glycohydrolase / NADP+ nucleosidase activity / NAD+ nucleosidase activity / defense response to virus / nucleotide binding Similarity search - Function | ||||||||||||||||||||||||||||||||||||
Biological species | Sphingobacterium faecium (bacteria) | ||||||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||||||||||||||||||||||||||
Authors | Morehouse BR / Yip MCJ / Keszei AFA / McNamara-Bordewick NK / Shao S / Kranzusch PJ | ||||||||||||||||||||||||||||||||||||
Funding support | United States, 11 items
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Citation | Journal: Nature / Year: 2022 Title: Cryo-EM structure of an active bacterial TIR-STING filament complex. Authors: Benjamin R Morehouse / Matthew C J Yip / Alexander F A Keszei / Nora K McNamara-Bordewick / Sichen Shao / Philip J Kranzusch / Abstract: Stimulator of interferon genes (STING) is an antiviral signalling protein that is broadly conserved in both innate immunity in animals and phage defence in prokaryotes. Activation of STING requires ...Stimulator of interferon genes (STING) is an antiviral signalling protein that is broadly conserved in both innate immunity in animals and phage defence in prokaryotes. Activation of STING requires its assembly into an oligomeric filament structure through binding of a cyclic dinucleotide, but the molecular basis of STING filament assembly and extension remains unknown. Here we use cryogenic electron microscopy to determine the structure of the active Toll/interleukin-1 receptor (TIR)-STING filament complex from a Sphingobacterium faecium cyclic-oligonucleotide-based antiphage signalling system (CBASS) defence operon. Bacterial TIR-STING filament formation is driven by STING interfaces that become exposed on high-affinity recognition of the cognate cyclic dinucleotide signal c-di-GMP. Repeating dimeric STING units stack laterally head-to-head through surface interfaces, which are also essential for human STING tetramer formation and downstream immune signalling in mammals. The active bacterial TIR-STING structure reveals further cross-filament contacts that brace the assembly and coordinate packing of the associated TIR NADase effector domains at the base of the filament to drive NAD hydrolysis. STING interface and cross-filament contacts are essential for cell growth arrest in vivo and reveal a stepwise mechanism of activation whereby STING filament assembly is required for subsequent effector activation. Our results define the structural basis of STING filament formation in prokaryotic antiviral signalling. | ||||||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26617.map.gz | 16.6 MB | EMDB map data format | |
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Header (meta data) | emd-26617-v30.xml emd-26617.xml | 18.8 KB 18.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26617_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_26617.png | 232 KB | ||
Filedesc metadata | emd-26617.cif.gz | 5.8 KB | ||
Others | emd_26617_additional_1.map.gz emd_26617_half_map_1.map.gz emd_26617_half_map_2.map.gz | 60.2 MB 115.9 MB 115.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26617 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26617 | HTTPS FTP |
-Validation report
Summary document | emd_26617_validation.pdf.gz | 969.9 KB | Display | EMDB validaton report |
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Full document | emd_26617_full_validation.pdf.gz | 969.5 KB | Display | |
Data in XML | emd_26617_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | emd_26617_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26617 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26617 | HTTPS FTP |
-Related structure data
Related structure data | 7un9MC 7un8C 7unaC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_26617.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | SfSTING with c-di-GMP double fiber sharpened map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: SfSTING with c-di-GMP double fiber unsharpened map
File | emd_26617_additional_1.map | ||||||||||||
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Annotation | SfSTING with c-di-GMP double fiber unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: SfSTING with c-di-GMP double fiber half map 1
File | emd_26617_half_map_1.map | ||||||||||||
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Annotation | SfSTING with c-di-GMP double fiber half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: SfSTING with c-di-GMP double fiber half map 2
File | emd_26617_half_map_2.map | ||||||||||||
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Annotation | SfSTING with c-di-GMP double fiber half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SfSTING with c-di-GMP double fiber
Entire | Name: SfSTING with c-di-GMP double fiber |
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Components |
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-Supramolecule #1: SfSTING with c-di-GMP double fiber
Supramolecule | Name: SfSTING with c-di-GMP double fiber / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Sphingobacterium faecium (bacteria) |
-Macromolecule #1: CD-NTase-associated protein 12
Macromolecule | Name: CD-NTase-associated protein 12 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: NAD+ glycohydrolase |
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Source (natural) | Organism: Sphingobacterium faecium (bacteria) |
Molecular weight | Theoretical: 34.30257 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)IL ...String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)IL IATKDDLTKQ RGESLTKPRD NVVFEFGLFL GAAGPEKCYL IAE(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) EDTDLP TDLDGITVAK FTRNSGQYNS LDKIVESIRT HLVKIAEMSQ LGLLPSTALA IGYYNSFIKR VCEEIHGSEC VELE GKKIK VKSFRVDVVI PETLDDNGVG NFTTLYNKRY GLSKATTCTN PALLGTRGFP FHFKVDPPDA NQESPVDIHL LDIPS TLST IVESLKLYLP SNQVGQDFDM DYLEMRELEN FAKVLKYLIG RNAATKGYVN VLTNVKL UniProtKB: CD-NTase-associated protein 12 |
-Macromolecule #2: 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydr...
Macromolecule | Name: 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) type: ligand / ID: 2 / Number of copies: 6 / Formula: C2E |
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Molecular weight | Theoretical: 690.411 Da |
Chemical component information | ChemComp-C2E: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |