[English] 日本語
Yorodumi
- EMDB-11634: Aquifex aeolicus lumazine synthase-derived nucleocapsid variant NC-3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11634
TitleAquifex aeolicus lumazine synthase-derived nucleocapsid variant NC-3
Map datapostprocessed masked map
Sample
  • Cell: Nucleocapsid NC-3
    • Protein or peptide: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase
Keywordscapsid / 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 / riboflavin biosynthetic process / RNA polymerase binding / transcription antitermination factor activity, RNA binding / bacterial-type RNA polymerase core enzyme 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 / riboflavin biosynthetic process / RNA polymerase binding / transcription antitermination factor activity, RNA binding / bacterial-type RNA polymerase core enzyme 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 / cytoplasm / 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: 7.04 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-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0509
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0509
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7a4i
  • Surface level: 0.0509
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7a4i
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11634.png

Downloads & links

-
Map

FileDownload / File: emd_11634.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpostprocessed masked map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.8 Å/pix.
x 360 pix.
= 648. Å		1.8 Å/pix.
x 360 pix.
= 648. Å		1.8 Å/pix.
x 360 pix.
= 648. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0509 / Movie #1: 0.0509
Minimum - Maximum-0.07406308 - 0.18504971
Average (Standard dev.)0.00062450784 (±0.009026477)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 648.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.81.81.8
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z648.000648.000648.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0740.1850.001

-
Supplemental data

-
Mask #1

Fileemd_11634_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 2

Fileemd_11634_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 1

Fileemd_11634_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Nucleocapsid NC-3

EntireName: Nucleocapsid NC-3
Components
  • Cell: Nucleocapsid NC-3
    • Protein or peptide: Antitermination protein N,6,7-dimethyl-8-ribityllumazine synthase,6,7-dimethyl-8-ribityllumazine synthase

-
Supramolecule #1: Nucleocapsid NC-3

SupramoleculeName: 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
Source (natural)Organism: Escherichia virus lambda

-
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: 240 / Enantiomer: LEVO / EC number: 6,7-dimethyl-8-ribityllumazine synthase
Source (natural)Organism: Aquifex aeolicus VF5 (bacteria)
Molecular weightTheoretical: 21.502309 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 22 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm 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 beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 32411
Startup modelType of model: INSILICO MODEL
In silico model: generated in RELION from the data themselves
Details: with icosahedral symmetry imposed (I1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 7.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 3815
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 550
Output model

PDB-7a4i:
Aquifex aeolicus lumazine synthase-derived nucleocapsid variant NC-3

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more