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

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Open data


ID or keywords:

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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
CitationJournal: 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-
UpdateApr 29, 2026-
Current statusApr 29, 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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