+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26618 | ||||||||||||||||||||||||||||||||||||
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Title | SfSTING with cGAMP (masked) | ||||||||||||||||||||||||||||||||||||
Map data | SfSTING with cGAMP (masked) sharpened map | ||||||||||||||||||||||||||||||||||||
Sample |
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Keywords | STING / bacterial / filament / ANTIVIRAL PROTEIN | ||||||||||||||||||||||||||||||||||||
Function / homology | Prokaryotic STING domain / Prokaryotic STING domain / CD-NTase-associated protein 12/Pycsar effector protein, TIR domain / CAP12/Pycsar effector protein, TIR domain / NAD+ glycohydrolase / NAD+ nucleosidase activity / defense response to virus / nucleotide binding / CD-NTase-associated protein 12 Function and homology information | ||||||||||||||||||||||||||||||||||||
Biological species | Sphingobacterium faecium (bacteria) | ||||||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 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_26618.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-26618-v30.xml emd-26618.xml | 18.4 KB 18.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26618_fsc.xml | 10 KB | Display | FSC data file |
Images | emd_26618.png | 119.1 KB | ||
Filedesc metadata | emd-26618.cif.gz | 5.8 KB | ||
Others | emd_26618_additional_1.map.gz emd_26618_half_map_1.map.gz emd_26618_half_map_2.map.gz | 65.3 MB 65.3 MB 65.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26618 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26618 | HTTPS FTP |
-Related structure data
Related structure data | 7unaMC 7un8C 7un9C M: atomic model generated by this map C: citing same article (ref.) |
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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_26618.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | SfSTING with cGAMP (masked) sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: SfSTING with cGAMP (masked) unsharpened map
File | emd_26618_additional_1.map | ||||||||||||
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Annotation | SfSTING with cGAMP (masked) unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: SfSTING with cGAMP (masked) half map 1
File | emd_26618_half_map_1.map | ||||||||||||
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Annotation | SfSTING with cGAMP (masked) half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: SfSTING with cGAMP (masked) half map 2
File | emd_26618_half_map_2.map | ||||||||||||
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Annotation | SfSTING with cGAMP (masked) half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SfSTING with cGAMP
Entire | Name: SfSTING with cGAMP |
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Components |
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-Supramolecule #1: SfSTING with cGAMP
Supramolecule | Name: SfSTING with cGAMP / 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: 8 / Enantiomer: LEVO / EC number: NAD+ glycohydrolase |
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Source (natural) | Organism: Sphingobacterium faecium (bacteria) |
Molecular weight | Theoretical: 36.956051 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MHHHHHHGSK KRIFIGSSSE QLTILNEIVD LLGDDVECIP WTDAFALNKS GLDSLIKQTR LADYSILIAT KDDLTKQRGE SLTKPRDNV VFEFGLFLGA AGPEKCYLIA EEDTDLPTDL DGITVAKFTR NSGQYNSLDK IVESIRTHLV KIAEMSQLGL L PSTALAIG ...String: MHHHHHHGSK KRIFIGSSSE QLTILNEIVD LLGDDVECIP WTDAFALNKS GLDSLIKQTR LADYSILIAT KDDLTKQRGE SLTKPRDNV VFEFGLFLGA AGPEKCYLIA EEDTDLPTDL DGITVAKFTR NSGQYNSLDK IVESIRTHLV KIAEMSQLGL L PSTALAIG YYNSFIKRVC EEIHGSECVE LEGKKIKVKS FRVDVVIPET LDDNGVGNFT TLYNKRYGLS KATTCTNPAL LG TRGFPFH FKVDPPDANQ ESPVDIHLLD IPSTLSTIVE SLKLYLPSNQ VGQDFDMDYL EMRELENFAK VLKYLIGRNA ATK GYVNVL TNVKL UniProtKB: CD-NTase-associated protein 12 |
-Macromolecule #2: 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-...
Macromolecule | Name: 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- ...Name: 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 type: ligand / ID: 2 / Number of copies: 4 / Formula: 4BW |
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Molecular weight | Theoretical: 674.411 Da |
Chemical component information | ChemComp-4BW: |
-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 TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.4000000000000001 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.9 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |