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- EMDB-56772: split variant of Aquifex aeolicus lumazine synthase-derived nucle... -

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Basic information

Entry
Database: EMDB / ID: EMD-56772
Titlesplit variant of Aquifex aeolicus lumazine synthase-derived nucleocapsid variant NC-4
Map data
Sample
  • Complex: Nucleocapsid NC-4
    • Complex: Nucleocapsid NC-4, N-terminal segments
    • Protein or peptide: 6,7-dimethyl-8-ribityllumazine synthase
    • Protein or peptide: 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 / cytoplasm / cytosol
Similarity search - Function
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
Similarity search - Component
Biological speciesEscherichia virus lambda / Aquifex aeolicus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsTetter S / Hilvert D
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-AdG-2012-321295European Union
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2026
Title: An engineered closed-shell, two-component, 480-subunit nucleocapsid.
Authors: Mikail D Levasseur / Naohiro Terasaka / Angela Steinauer / Stephan Tetter / Sara Pfister / Beat H Meier / Donald Hilvert /
Abstract: Self-assembling protein cages are valuable nanoscale containers for biotechnology and medical applications. Two-component systems are especially attractive due to their potential for functional ...Self-assembling protein cages are valuable nanoscale containers for biotechnology and medical applications. Two-component systems are especially attractive due to their potential for functional complexity. In this study, we demonstrate that the subunits of the 240-subunit nucleocapsid NC-4, which was previously evolved to package and protect its encoding mRNA, can be split into two fragments without disrupting cage assembly or structure, generating a two-component, 480-subunit capsid. This modification introduces additional termini on the cage's exterior surface, creating opportunities for functionalization. We exploited these new sites by genetically appending peptide and protein tags to the exterior surface of split NC-4 (spNC-4), enabling site-specific glycosylation via posttranslational modification and cell-specific delivery by targeted antibody recruitment. Our findings broaden the utility of the NC-4 nucleocapsid. By extension, splitting related protein compartments that bind diverse cargoes could offer a robust platform for biotechnological applications requiring simultaneous encapsulation and customizable surface modification.
#1: Journal: Biorxiv / Year: 2025
Title: An engineered closed-shell, two-component, 480-subunit nucleocapsid
Authors: Levasseur MD / Terasaka N / Steinauer A / Tetter S / Pfister S / Meier BH / Hilvert D
History
DepositionFeb 16, 2026-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56772.png

Downloads & links

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Map

FileDownload / File: emd_56772.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 500 pix.
= 550. Å		1.1 Å/pix.
x 500 pix.
= 550. Å		1.1 Å/pix.
x 500 pix.
= 550. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.18305616 - 0.3591892
Average (Standard dev.)0.00062467565 (±0.011341801)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 550.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56772_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_56772_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_56772_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Nucleocapsid NC-4

EntireName: Nucleocapsid NC-4
Components
  • Complex: Nucleocapsid NC-4
    • Complex: Nucleocapsid NC-4, N-terminal segments
    • Protein or peptide: 6,7-dimethyl-8-ribityllumazine synthase
    • Protein or peptide: 6,7-dimethyl-8-ribityllumazine synthase

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Supramolecule #1: Nucleocapsid NC-4

SupramoleculeName: Nucleocapsid NC-4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Evolved and split variant of a virus-inspired nucleocapsid design based on the Aquifex aeolicus riboflavin synthase

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Supramolecule #2: Nucleocapsid NC-4, N-terminal segments

SupramoleculeName: Nucleocapsid NC-4, N-terminal segments / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Escherichia virus lambda

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Macromolecule #1: 6,7-dimethyl-8-ribityllumazine synthase

MacromoleculeName: 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 (bacteria)
Molecular weightTheoretical: 12.324837 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGNARTRRRE RRAEKQAQWK AANAGAGAGA MATPHFDYNA SVVSKGLANL SLELRKPVSF DIITADTLEQ AIERAGTKHG NKGWEAALS AIEMANLYKS LRGTEHHHHL HGSS

UniProtKB: 6,7-dimethyl-8-ribityllumazine synthase

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Macromolecule #2: 6,7-dimethyl-8-ribityllumazine synthase

MacromoleculeName: 6,7-dimethyl-8-ribityllumazine synthase / type: protein_or_peptide / ID: 2 / Number of copies: 240 / Enantiomer: LEVO / EC number: 6,7-dimethyl-8-ribityllumazine synthase
Source (natural)Organism: Aquifex aeolicus (bacteria)
Molecular weightTheoretical: 9.356705 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGIEIYEGKL TAEGLRFGIV ASRFNHTLVD RLVEGAIDCI VRHGGRGEDI TLVRVPGAWE IPVAADELAR KEDIDAVIAF GDLIRG

UniProtKB: 6,7-dimethyl-8-ribityllumazine synthase

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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

Concentration2 mg/mL
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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 69723
CTF correctionSoftware - Name: Gctf (ver. 1.06) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: generated in RELION from the data themselves
Details: with icosahedral symmetry imposed (I1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 20021
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)

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Atomic model buiding 1

Initial modelPDB ID:

1hqk


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 66.9
Output model

PDB-28ro:
split variant of Aquifex aeolicus lumazine synthase-derived nucleocapsid variant NC-4

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