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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Retron-Eco1 filament (2 segments) | |||||||||
![]() | Retron-Eco1 filament (No Ligand) Main MAP Unsharpened | |||||||||
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![]() | retron / IMMUNE SYSTEM / N-glycosidase / DNA-RNA-Protein complex | |||||||||
Function / homology | ![]() RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / defense response to virus / RNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.41 Å | |||||||||
![]() | Carabias del Rey A / Montoya G | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Retron-Eco1 assembles NAD-hydrolyzing filaments that provide immunity against bacteriophages. Authors: Arturo Carabias / Sarah Camara-Wilpert / Mario Rodríguez Mestre / Blanca Lopéz-Méndez / Ivo A Hendriks / Ruiliang Zhao / Tillmann Pape / Anders Fuglsang / Sean Hoi-Ching Luk / Michael L ...Authors: Arturo Carabias / Sarah Camara-Wilpert / Mario Rodríguez Mestre / Blanca Lopéz-Méndez / Ivo A Hendriks / Ruiliang Zhao / Tillmann Pape / Anders Fuglsang / Sean Hoi-Ching Luk / Michael L Nielsen / Rafael Pinilla-Redondo / Guillermo Montoya / ![]() Abstract: Retrons are toxin-antitoxin systems protecting bacteria against bacteriophages via abortive infection. The Retron-Eco1 antitoxin is formed by a reverse transcriptase (RT) and a non-coding RNA (ncRNA) ...Retrons are toxin-antitoxin systems protecting bacteria against bacteriophages via abortive infection. The Retron-Eco1 antitoxin is formed by a reverse transcriptase (RT) and a non-coding RNA (ncRNA)/multi-copy single-stranded DNA (msDNA) hybrid that neutralizes an uncharacterized toxic effector. Yet, the molecular mechanisms underlying phage defense remain unknown. Here, we show that the N-glycosidase effector, which belongs to the STIR superfamily, hydrolyzes NAD during infection. Cryoelectron microscopy (cryo-EM) analysis shows that the msDNA stabilizes a filament that cages the effector in a low-activity state in which ADPr, a NAD hydrolysis product, is covalently linked to the catalytic E106 residue. Mutations shortening the msDNA induce filament disassembly and the effector's toxicity, underscoring the msDNA role in immunity. Furthermore, we discovered a phage-encoded Retron-Eco1 inhibitor (U56) that binds ADPr, highlighting the intricate interplay between retron systems and phage evolution. Our work outlines the structural basis of Retron-Eco1 defense, uncovering ADPr's pivotal role in immunity. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 407.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.7 KB 21.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 20 KB | Display | ![]() |
Images | ![]() | 63.8 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 765 MB 765 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 27.7 KB | Display | |
Data in CIF | ![]() | 35.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8qbkC ![]() 8qblC ![]() 8qbmC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Retron-Eco1 filament (No Ligand) Main MAP Unsharpened | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Retron-Eco1 filament (No Ligand) Half Map A
File | emd_18317_half_map_1.map | ||||||||||||
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Annotation | Retron-Eco1 filament (No Ligand) Half Map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Retron-Eco1 filament (No Ligand) Half Map B
File | emd_18317_half_map_2.map | ||||||||||||
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Annotation | Retron-Eco1 filament (No Ligand) Half Map B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Filamentous Assembly containing Retron-Eco1 RT:ncRNA-msDNA:Effect...
Entire | Name: Filamentous Assembly containing Retron-Eco1 RT:ncRNA-msDNA:Effector with a stoichiometry of 2:2:2 per repetitive unit - 2 segments |
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Components |
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-Supramolecule #1: Filamentous Assembly containing Retron-Eco1 RT:ncRNA-msDNA:Effect...
Supramolecule | Name: Filamentous Assembly containing Retron-Eco1 RT:ncRNA-msDNA:Effector with a stoichiometry of 2:2:2 per repetitive unit - 2 segments type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #4-#6 Details: Filament as purified from the bacteria after overexpression. No ligand added. |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 21 kDa/nm |
-Macromolecule #1: Retron-Eco1 Reverse Transcriptase
Macromolecule | Name: Retron-Eco1 Reverse Transcriptase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKSAEYLNTF RLRNLGLPVM NNLHDMSKAT RISVETLRLL IYTADFRYRI YTVEKKGPEK RMRTIYQPSR ELKALQGWVL RNILDKLSSS PFSIGFEKHQ SILNNATPHI GANFILNIDL EDFFPSLTAN KVFGVFHSLG YNRLISSVLT KICCYKNLLP QGAPSSPKLA ...String: MKSAEYLNTF RLRNLGLPVM NNLHDMSKAT RISVETLRLL IYTADFRYRI YTVEKKGPEK RMRTIYQPSR ELKALQGWVL RNILDKLSSS PFSIGFEKHQ SILNNATPHI GANFILNIDL EDFFPSLTAN KVFGVFHSLG YNRLISSVLT KICCYKNLLP QGAPSSPKLA NLICSKLDYR IQGYAGSRGL IYTRYADDLT LSAQSMKKVV KARDFLFSII PSEGLVINSK KTCISGPRSQ RKVTGLVISQ EKVGIGREKY KEIRAKIHHI FCGKSSEIEH VRGWLSFILS VDSKSHRRLI TYISKLEKKY GKNPLNKAKT GSEFELENLY FQGELRRQAS ALEHHHHHH UniProtKB: Retron Ec86 reverse transcriptase |
-Macromolecule #4: Retron-Eco1 Effector
Macromolecule | Name: Retron-Eco1 Effector / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MNKKFTDEQQ QQLIGHLTKK GFYRGANIKI TIFLCGGDVA NHQSWRHQLS QFLAKFSDVD IFYPEDLFDD LLAGQGQHSL LSLENILAEA VDVIILFPES PGSFTELGAF SNNENLRRKL ICIQDAKFKS KRSFINYGPV RLLRKFNSKS VLRCSSNELK EMCDSSIDVA ...String: MNKKFTDEQQ QQLIGHLTKK GFYRGANIKI TIFLCGGDVA NHQSWRHQLS QFLAKFSDVD IFYPEDLFDD LLAGQGQHSL LSLENILAEA VDVIILFPES PGSFTELGAF SNNENLRRKL ICIQDAKFKS KRSFINYGPV RLLRKFNSKS VLRCSSNELK EMCDSSIDVA RKLRLYKKLM ASIKKVRKEN KVSKDIGNIL YAERFLLPCI YLLDSVNYRT LCELAFKAIK QDDVLSKIIV RSVVSRLINE RKILQMTDGY QVTALGASYV RSVFDRKTLD RLRLEIMNFE NRRKSTFNYD KIPYAHP UniProtKB: Retron Ec86 putative ribosyltransferase/DNA-binding protein |
-Macromolecule #2: Retron-Eco1-msr
Macromolecule | Name: Retron-Eco1-msr / type: rna / ID: 2 |
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Source (natural) | Organism: ![]() ![]() |
Sequence | String: AUGCGCACCC UUAGCGAGAG GUUUAUCAUU AAGGUCAACC UCUGGAUGUU GUUUCGGCAU CCUGCAUUGA AUCUGAGUUA CU |
-Macromolecule #6: Retron-Eco1-A2
Macromolecule | Name: Retron-Eco1-A2 / type: rna / ID: 6 |
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Source (natural) | Organism: ![]() ![]() |
Sequence | String: CGUAAGGGUG CGCA |
-Macromolecule #5: Retron-Eco1 msDNA
Macromolecule | Name: Retron-Eco1 msDNA / type: other / ID: 5 Classification: polydeoxyribonucleotide/polyribonucleotide hybrid |
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Source (natural) | Organism: ![]() ![]() |
Sequence | String: GTCAGAAAAA ACGGGTTTCC TGGTTGGCTC GGAGAGCATC AGGCGATGCT CTCCGTTCCA ACAAGGAAAA CAGACAGTAA CTCAG |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 7.5 Component:
Details: 20 mM HEPES (pH 7.5),200 mM KCl, 5 mM MgCl2, 1mM TCEP | ||||||||||
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Details: 10 mAmp | ||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blotting time 3 seconds. | ||||||||||
Details | The complex was prepared at a concentration corresponding to A260nm = ~9 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 4465 / Average electron dose: 39.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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