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- EMDB-11634: Aquifex aeolicus lumazine synthase-derived nucleocapsid variant NC-3 -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11634 | |||||||||
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Title | Aquifex aeolicus lumazine synthase-derived nucleocapsid variant NC-3 | |||||||||
![]() | postprocessed masked map | |||||||||
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![]() | capsid / design / virus mimic / VIRUS LIKE PARTICLE | |||||||||
Function / homology | ![]() 6,7-dimethyl-8-ribityllumazine synthase / 6,7-dimethyl-8-ribityllumazine synthase activity / riboflavin synthase complex / bacterial-type RNA polymerase core enzyme binding / riboflavin biosynthetic process / RNA polymerase binding / transcription antitermination factor activity, RNA binding / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination ...6,7-dimethyl-8-ribityllumazine synthase / 6,7-dimethyl-8-ribityllumazine synthase activity / riboflavin synthase complex / bacterial-type RNA polymerase core enzyme binding / riboflavin biosynthetic process / RNA polymerase binding / transcription antitermination factor activity, RNA binding / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / RNA stem-loop binding / single-stranded RNA binding / regulation of transcription by RNA polymerase II / DNA binding / RNA binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.04 Å | |||||||||
![]() | Tetter S / Hilvert D | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Evolution of a virus-like architecture and packaging mechanism in a repurposed bacterial protein. Authors: Stephan Tetter / Naohiro Terasaka / Angela Steinauer / Richard J Bingham / Sam Clark / Andrew J P Scott / Nikesh Patel / Marc Leibundgut / Emma Wroblewski / Nenad Ban / Peter G Stockley / ...Authors: Stephan Tetter / Naohiro Terasaka / Angela Steinauer / Richard J Bingham / Sam Clark / Andrew J P Scott / Nikesh Patel / Marc Leibundgut / Emma Wroblewski / Nenad Ban / Peter G Stockley / Reidun Twarock / Donald Hilvert / ![]() ![]() Abstract: Viruses are ubiquitous pathogens of global impact. Prompted by the hypothesis that their earliest progenitors recruited host proteins for virion formation, we have used stringent laboratory evolution ...Viruses are ubiquitous pathogens of global impact. Prompted by the hypothesis that their earliest progenitors recruited host proteins for virion formation, we have used stringent laboratory evolution to convert a bacterial enzyme that lacks affinity for nucleic acids into an artificial nucleocapsid that efficiently packages and protects multiple copies of its own encoding messenger RNA. Revealing remarkable convergence on the molecular hallmarks of natural viruses, the accompanying changes reorganized the protein building blocks into an interlaced 240-subunit icosahedral capsid that is impermeable to nucleases, and emergence of a robust RNA stem-loop packaging cassette ensured high encapsidation yields and specificity. In addition to evincing a plausible evolutionary pathway for primordial viruses, these findings highlight practical strategies for developing nonviral carriers for diverse vaccine and delivery applications. #1: ![]() Title: Evolution of a virus-like architecture and packaging mechanism in a repurposed bacterial protein Authors: Tetter S / Terasaka N / Steinauer A / Bingham RJ / Clark S / Scott AJP / Patel N / Leibundgut M / Wroblewski E / Ban N / Stockley PG / Twarock R / Hilvert D | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 24.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.4 KB 19.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.8 KB | Display | ![]() |
Images | ![]() | 99.4 KB | ||
Masks | ![]() | 178 MB | ![]() | |
Filedesc metadata | ![]() | 6.1 KB | ||
Others | ![]() ![]() | 139.5 MB 139.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7a4iMC ![]() 7a4fC ![]() 7a4gC ![]() 7a4hC ![]() 7a4jC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | postprocessed masked map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_11634_half_map_1.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_11634_half_map_2.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Nucleocapsid NC-3
Entire | Name: Nucleocapsid NC-3 |
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Components |
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-Supramolecule #1: Nucleocapsid NC-3
Supramolecule | Name: Nucleocapsid NC-3 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all Details: Evolved variant of a virus-inspired nucleocapsid design based on the Aquifex aeolicus riboflavin synthase |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase...
Macromolecule | Name: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase type: protein_or_peptide / ID: 1 / Number of copies: 240 / Enantiomer: LEVO / EC number: 6,7-dimethyl-8-ribityllumazine synthase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 21.502309 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGNAKTRRRE RRAEKQAQWK AANAGAGAGA MATPHFDYNA SVVSKGLANL SLELRKPVTF DIITADTLEQ AIERAGTKHG NKGWEAALS AIEMANLYKS LRGTGHHHHH HGSSIEIYEG KLTAEGLRFG IVASRFNHTL VDRLVEGAID CIVRHGGREE D ITLVRVPG ...String: MGNAKTRRRE RRAEKQAQWK AANAGAGAGA MATPHFDYNA SVVSKGLANL SLELRKPVTF DIITADTLEQ AIERAGTKHG NKGWEAALS AIEMANLYKS LRGTGHHHHH HGSSIEIYEG KLTAEGLRFG IVASRFNHTL VDRLVEGAID CIVRHGGREE D ITLVRVPG SWEIPVAADE LARKEDIDAV IAFGDLIRG UniProtKB: Antitermination protein N, 6,7-dimethyl-8-ribityllumazine synthase, 6,7-dimethyl-8-ribityllumazine synthase |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 22 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 1-7 / Number real images: 134 / Average electron dose: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 62000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 550 |
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Output model | ![]() PDB-7a4i: |