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- EMDB-51006: Circularly permuted lumazine synthase 12-pentamer spherical cage -

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Basic information

Entry
Database: EMDB / ID: EMD-51006
TitleCircularly permuted lumazine synthase 12-pentamer spherical cage
Map dataCombined half maps post-processed by DeepEMhancer with highRes normalization mode.
Sample
  • Complex: Circularly permuted lumazine synthase 12-pentamer spherical cage
    • Protein or peptide: 6,7-dimethyl-8-ribityllumazine synthase
Keywordsprotein cage / protein engineering / self-assembly / geometry / helical reconstruction / bionanotechnology / polymorphism / pentamer / DE NOVO PROTEIN
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 / cytosol / cytoplasm
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 speciesAquifex aeolicus VF5 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.08 Å
AuthorsKoziej L / Azuma Y
Funding support Poland, European Union, 3 items
OrganizationGrant numberCountry
Polish National Science Centre2018/31/D/NZ1/01102 Poland
Polish National Science Centre2019/35/B/NZ1/02044 Poland
European Molecular Biology Organization (EMBO)EMBO Installation Grant (YA)European Union
CitationJournal: ACS Nano / Year: 2025
Title: Dynamic Assembly of Pentamer-Based Protein Nanotubes.
Authors: Lukasz Koziej / Farzad Fatehi / Marta Aleksejczuk / Matthew J Byrne / Jonathan G Heddle / Reidun Twarock / Yusuke Azuma /
Abstract: Hollow proteinaceous particles are useful nanometric containers for delivery and catalysis. Understanding the molecular mechanisms and the geometrical theory behind the polymorphic protein assemblies ...Hollow proteinaceous particles are useful nanometric containers for delivery and catalysis. Understanding the molecular mechanisms and the geometrical theory behind the polymorphic protein assemblies provides a basis for designing ones with the desired morphology. As such, we found that a circularly permuted variant of a cage-forming enzyme, lumazine synthase, cpAaLS, assembles into a variety of hollow spherical and cylindrical structures in response to changes in ionic strength. Cryogenic electron microscopy revealed that these structures are composed entirely of pentameric subunits, and the dramatic cage-to-tube transformation is attributed to the moderately hindered 3-fold symmetry interaction and the imparted torsion angle of the building blocks, where both mechanisms are mediated by an α-helix domain that is untethered from the native position by circular permutation. Mathematical modeling suggests that the unique double- and triple-stranded helical arrangements of subunits are optimal tiling patterns, while different geometries should be possible by modulating the interaction angles of the pentagons. These structural insights into dynamic, pentamer-based protein cages and nanotubes afford guidelines for designing nanoarchitectures with customized morphology and assembly characteristics.
History
DepositionJul 12, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51006.png

Downloads & links

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Map

FileDownload / File: emd_51006.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCombined half maps post-processed by DeepEMhancer with highRes normalization mode.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 280 pix.
= 240.8 Å		0.86 Å/pix.
x 280 pix.
= 240.8 Å		0.86 Å/pix.
x 280 pix.
= 240.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.042800862 - 1.6893263
Average (Standard dev.)0.011388651 (±0.078166224)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 240.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51006_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Map combined from 2 independent halves. Not post-processed.

Fileemd_51006_additional_1.map
AnnotationMap combined from 2 independent halves. Not post-processed.
Projections & Slices
AxesZYX

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Additional map: Combined half maps post-processed using sharpening B factor 65.0.

Fileemd_51006_additional_2.map
AnnotationCombined half maps post-processed using sharpening B factor 65.0.
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

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Half map: #1

Fileemd_51006_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_51006_half_map_2.map
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Sample components

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Entire : Circularly permuted lumazine synthase 12-pentamer spherical cage

EntireName: Circularly permuted lumazine synthase 12-pentamer spherical cage
Components
  • Complex: Circularly permuted lumazine synthase 12-pentamer spherical cage
    • Protein or peptide: 6,7-dimethyl-8-ribityllumazine synthase

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Supramolecule #1: Circularly permuted lumazine synthase 12-pentamer spherical cage

SupramoleculeName: Circularly permuted lumazine synthase 12-pentamer spherical cage
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Circularly permuted (84) variant of Aquifex aeolicus lumazine synthase
Source (natural)Organism: Aquifex aeolicus VF5 (bacteria)

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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 / Details: cpAaLS(84),cpAaLS(84) / Number of copies: 60 / Enantiomer: LEVO / EC number: 6,7-dimethyl-8-ribityllumazine synthase
Source (natural)Organism: Aquifex aeolicus VF5 (bacteria)
Molecular weightTheoretical: 17.449938 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MATPHFDYIA SEVSKGLANL SLELRKPITF GVITADTLEQ AIERAGTKHG NKGWEAALSA IEMANLFKSL RGTGGSGSSM EIYEGKLTA EGLRFGIVAS RFNHALVDRL VEGAIDCIVR HGGREEDITL VRVPGSWEIP VAAGELARKE DIDAVIAIGV L IRG

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

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMTris-HCltris(hydroxymethyl)aminomethane
150.0 mMNaClsodium chloride
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 8486 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.9 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 590975 / Details: Template picking
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.08 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 98492
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) / Details: Ab initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) / Details: 3D auto-refine
Final 3D classificationNumber classes: 4 / Avg.num./class: 100000 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1hqk


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsInitial fitting was done using ChimeraX. Flexible fitting was done using Isolde.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9g3p:
Circularly permuted lumazine synthase 12-pentamer spherical cage

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