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- EMDB-11632: Aquifex aeolicus lumazine synthase-derived nucleocapsid variant N... -

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Basic information

Entry
Database: EMDB / ID: EMD-11632
TitleAquifex aeolicus lumazine synthase-derived nucleocapsid variant NC-1 (180-mer)
Map datamap postprocessed in Relion
Sample
  • Complex: Aquifex aeolicus lumazine synthase-derived nucleocapsid variant NC-1 (180-mer)
    • Protein or peptide: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
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
Antitermination protein N, arginine-rich motif / 36-mer N-terminal peptide of the N protein (N36) / Lumazine synthase / Lumazine/riboflavin synthase / Lumazine/riboflavin synthase superfamily / 6,7-dimethyl-8-ribityllumazine synthase
Similarity search - Domain/homology
6,7-dimethyl-8-ribityllumazine synthase / Antitermination protein N
Similarity search - Component
Biological speciesEscherichia virus lambda / Aquifex aeolicus VF5 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsTetter S / Hilvert D
Funding support1 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-AdG-2012-321295
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
DepositionAug 19, 2020-
Header (metadata) releaseJun 2, 2021-
Map releaseJun 2, 2021-
UpdateJun 23, 2021-
Current statusJun 23, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
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  • Surface view with fitted model
  • Atomic models: PDB-7a4g
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7a4g
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11632.png

Downloads & links

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Map

FileDownload / File: emd_11632.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap postprocessed in Relion
Voxel sizeX=Y=Z: 1.375 Å
Density
Contour LevelBy AUTHOR: 0.0373 / Movie #1: 0.05
Minimum - Maximum-0.15485176 - 0.2716634
Average (Standard dev.)0.0004619545 (±0.009382004)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 550.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3751.3751.375
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z550.000550.000550.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1550.2720.000

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Supplemental data

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Mask #1

Fileemd_11632_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: map from 3D autorefinement in Relion

Fileemd_11632_additional_1.map
Annotationmap from 3D autorefinement in Relion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_11632_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_11632_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Aquifex aeolicus lumazine synthase-derived nucleocapsid variant N...

EntireName: Aquifex aeolicus lumazine synthase-derived nucleocapsid variant NC-1 (180-mer)
Components
  • Complex: Aquifex aeolicus lumazine synthase-derived nucleocapsid variant NC-1 (180-mer)
    • Protein or peptide: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase

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Supramolecule #1: Aquifex aeolicus lumazine synthase-derived nucleocapsid variant N...

SupramoleculeName: Aquifex aeolicus lumazine synthase-derived nucleocapsid variant NC-1 (180-mer)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia virus lambda
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #1: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase...

MacromoleculeName: 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 weightTheoretical: 21.337312 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGNAKTRRRE RRAEKQAQWK AANAGAGAGA MATPHFDYIA SEVSKGLANL SLELRKPITF GVITADTLEQ AIERAGTKHG NKGWEAALS AIEMANLFKS LRGTGHHHHH HGSSMEIYEG KLTAEGLRFG IVASRFNHAL VDRLVEGAID CIVRHGGREE D ITLVRVPG ...String:
MGNAKTRRRE RRAEKQAQWK AANAGAGAGA MATPHFDYIA SEVSKGLANL SLELRKPITF GVITADTLEQ AIERAGTKHG NKGWEAALS AIEMANLFKS LRGTGHHHHH HGSSMEIYEG KLTAEGLRFG IVASRFNHAL VDRLVEGAID CIVRHGGREE D ITLVRVPG SWEIPVAAGE LARKEDIDAV IAIGVLIRG

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 22 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 1481 / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 129954
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: INSILICO MODEL
In silico model: generated in RELION from the data themselves
Details: with tetrahedral symmetry imposed
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: T (tetrahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 5226
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1hqk


Chain - Chain ID: A
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 59
Output model

PDB-7a4g:
Aquifex aeolicus lumazine synthase-derived nucleocapsid variant NC-1 (180-mer)

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