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Yorodumi- PDB-7a4f: Aquifex aeolicus lumazine synthase-derived nucleocapsid variant N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a4f | ||||||
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Title | Aquifex aeolicus lumazine synthase-derived nucleocapsid variant NC-1 (120-mer) | ||||||
Components | Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase | ||||||
Keywords | VIRUS LIKE PARTICLE / capsid / design / virus mimic | ||||||
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 stem-loop binding / RNA polymerase binding / transcription antitermination factor activity, RNA binding / regulation of DNA-templated transcription elongation / transcription antitermination ...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 stem-loop binding / RNA polymerase binding / transcription antitermination factor activity, RNA binding / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Tetter, S. / Hilvert, D. | ||||||
Funding support | 1items
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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, R.J. / Clark, S. / Scott, A.J.P. / Patel, N. / Leibundgut, M. / Wroblewski, E. / Ban, N. / Stockley, P.G. / Twarock, R. / Hilvert, D. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7a4f.cif.gz | 2.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7a4f.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7a4f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/7a4f ftp://data.pdbj.org/pub/pdb/validation_reports/a4/7a4f | HTTPS FTP |
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-Related structure data
Related structure data | 11631MC 7a4gC 7a4hC 7a4iC 7a4jC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 21337.312 Da / Num. of mol.: 120 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia virus lambda, (gene. exp.) Aquifex aeolicus VF5 (bacteria) Gene: N, lambdap49, ribH, aq_132 / Variant: VF5 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P03045, UniProt: O66529, 6,7-dimethyl-8-ribityllumazine synthase |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Aquifex aeolicus lumazine synthase-derived nucleocapsid variant NC-1 (120-mer) Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | ||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 | ||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 22 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 60 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 129954 | ||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: T (tetrahedral) | ||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5257 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 91.6 / Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 1HQK Pdb chain-ID: A |