[English] 日本語
Yorodumi- EMDB-11633: Aquifex aeolicus lumazine synthase-derived nucleocapsid variant N... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11633 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Aquifex aeolicus lumazine synthase-derived nucleocapsid variant NC-2 (180-mer) | |||||||||
Map data | half map 1 | |||||||||
Sample |
| |||||||||
Keywords | capsid / design / virus mimic / VIRUS LIKE PARTICLE | |||||||||
Function / homology | Function and homology information 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 | Escherichia virus lambda / Aquifex aeolicus VF5 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Tetter S / Hilvert D | |||||||||
Funding support | 1 items
| |||||||||
Citation | Journal: Science / Year: 2021 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: Journal: Biorxiv / Year: 2021 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11633.map.gz | 31 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-11633-v30.xml emd-11633.xml | 22 KB 22 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11633_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_11633.png | 79 KB | ||
Masks | emd_11633_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-11633.cif.gz | 6.3 KB | ||
Others | emd_11633_additional_1.map.gz emd_11633_half_map_1.map.gz emd_11633_half_map_2.map.gz | 194.1 MB 194.2 MB 194.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11633 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11633 | HTTPS FTP |
-Validation report
Summary document | emd_11633_validation.pdf.gz | 993.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_11633_full_validation.pdf.gz | 993 KB | Display | |
Data in XML | emd_11633_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | emd_11633_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11633 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11633 | HTTPS FTP |
-Related structure data
Related structure data | 7a4hMC 7a4fC 7a4gC 7a4iC 7a4jC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_11633.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.375 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_11633_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: map from 3D autorefinement in Relion
File | emd_11633_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | map from 3D autorefinement in Relion | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: map from 3D autorefinement in Relion
File | emd_11633_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | map from 3D autorefinement in Relion | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map 2
File | emd_11633_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Aquifex aeolicus lumazine synthase-derived nucleocapsid variant N...
Entire | Name: Aquifex aeolicus lumazine synthase-derived nucleocapsid variant NC-2 (180-mer) |
---|---|
Components |
|
-Supramolecule #1: Aquifex aeolicus lumazine synthase-derived nucleocapsid variant N...
Supramolecule | Name: Aquifex aeolicus lumazine synthase-derived nucleocapsid variant NC-2 (180-mer) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Escherichia virus lambda |
-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: 180 / Enantiomer: LEVO / EC number: 6,7-dimethyl-8-ribityllumazine synthase |
---|---|
Source (natural) | Organism: Aquifex aeolicus VF5 (bacteria) |
Molecular weight | Theoretical: 21.41534 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MGNAKTRRRE RRAEKQAQWK AANAGAGAGA MATPHFDYIA SVVSKGLANL SLELRKPVTF DIITADTLEQ AIERAGTKHG NKGWEAALS AIEMANLFKS LRGTGHHHHH HGSSMEIYEG KLTAEGLRFG IVASRFNHAL VDRLVEGAID CIVRHGGREE D ITLVRVPG ...String: MGNAKTRRRE RRAEKQAQWK AANAGAGAGA MATPHFDYIA SVVSKGLANL SLELRKPVTF DIITADTLEQ AIERAGTKHG NKGWEAALS AIEMANLFKS LRGTGHHHHH HGSSMEIYEG KLTAEGLRFG IVASRFNHAL VDRLVEGAID CIVRHGGREE D ITLVRVPG SWEIPVAAGE 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 |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 22 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 848 / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |