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- EMDB-54383: Aquifex aeolicus lumazine synthase 11-pentamer cage in complex wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-54383
TitleAquifex aeolicus lumazine synthase 11-pentamer cage in complex with riboflavin synthase trimer
Map dataMap combined from 2 independent halves and not post-processed
Sample
  • Complex: Aquifex aeolicus lumazine synthase 11-pentamer cage in complex with riboflavin synthase trimer
    • Protein or peptide: Riboflavin synthase
    • Protein or peptide: 6,7-dimethyl-8-ribityllumazine synthase
Keywordsprotein cage / protein engineering / self-assembly / geometry / pentamer / encapsulation / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


riboflavin synthase / riboflavin synthase activity / 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-binding protein / Lumazine-binding domain / Lumazine binding domain / Riboflavin synthase alpha chain lumazine-binding repeat profile. / Lumazine synthase / Lumazine/riboflavin synthase / Lumazine/riboflavin synthase superfamily / 6,7-dimethyl-8-ribityllumazine synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / Riboflavin synthase-like beta-barrel
Similarity search - Domain/homology
6,7-dimethyl-8-ribityllumazine synthase / Riboflavin synthase
Similarity search - Component
Biological speciesAquifex aeolicus VF5 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsKoziej L / Azuma Y
Funding support Poland, European Union, 4 items
OrganizationGrant numberCountry
Polish National Science Centre2020/37/B/NZ1/01187 Poland
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: Nat Commun / Year: 2026
Title: A molecular basis for stoichiometric enzyme encapsulation in the vitamin B2 biosynthesis compartment.
Authors: Lukasz Koziej / Jedrzej Pankowski / Monika Stefanska / Daniel Jankowski / Agnieszka Gawin / V Vishal Malolan / Juha T Huiskonen / Takahiro Kosugi / Yusuke Azuma /
Abstract: Encapsulating metabolic enzymes within protein cages enhances catalytic efficiency through substrate channeling. The vitamin B2 biosynthesis system, in which a dodecahedral lumazine synthase (LS) ...Encapsulating metabolic enzymes within protein cages enhances catalytic efficiency through substrate channeling. The vitamin B2 biosynthesis system, in which a dodecahedral lumazine synthase (LS) cage encapsulates a homotrimeric riboflavin synthase (RS), exemplifies this strategy, yet the molecular basis for this stoichiometric enzyme encapsulation has remained elusive. Here, cryogenic electron microscopy structures reveal a hierarchical assembly mechanism that ensures the defined host-guest ratio. RS C-terminal cage-localization signal peptides anchor at LS pentamer-pentamer interfaces early during assembly, stabilizing open intermediates that, together with delayed later-stage cage closure, extend the loading window until guest incorporation is complete. RS spatial occupancy avoids overloading, while a molecular lock upon final closure prevents disassembly. The elucidated anchoring mechanism enabled structure-based phylogenetic analysis across diverse organisms, suggesting multiple independent evolutionary origins of this modular encapsulation strategy. This naturally occurring architecture provides design principles for engineering synthetic catalytic compartments with programmable stoichiometric control.
History
DepositionJul 15, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54383.png

Downloads & links

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Map

FileDownload / File: emd_54383.map.gz / Format: CCP4 / Size: 196.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap combined from 2 independent halves and not post-processed
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 372 pix.
= 314.563 Å		0.85 Å/pix.
x 372 pix.
= 314.563 Å		0.85 Å/pix.
x 372 pix.
= 314.563 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8456 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.088279285 - 0.2085102
Average (Standard dev.)0.0004032327 (±0.012135274)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions372372372
Spacing372372372
CellA=B=C: 314.5632 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54383_msk_1.map
Projections & Slices
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Additional map: Combined half maps symmetrized and post-processed using sharpening...

Fileemd_54383_additional_1.map
AnnotationCombined half maps symmetrized and post-processed using sharpening B factor 48.4
Projections & Slices
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Half map: #1

Fileemd_54383_half_map_1.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54383_half_map_2.map
Projections & Slices
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Sample components

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Entire : Aquifex aeolicus lumazine synthase 11-pentamer cage in complex wi...

EntireName: Aquifex aeolicus lumazine synthase 11-pentamer cage in complex with riboflavin synthase trimer
Components
  • Complex: Aquifex aeolicus lumazine synthase 11-pentamer cage in complex with riboflavin synthase trimer
    • Protein or peptide: Riboflavin synthase
    • Protein or peptide: 6,7-dimethyl-8-ribityllumazine synthase

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Supramolecule #1: Aquifex aeolicus lumazine synthase 11-pentamer cage in complex wi...

SupramoleculeName: Aquifex aeolicus lumazine synthase 11-pentamer cage in complex with riboflavin synthase trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Aquifex aeolicus VF5 (bacteria)
Molecular weightTheoretical: 1.07 MDa

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Macromolecule #1: Riboflavin synthase

MacromoleculeName: Riboflavin synthase / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: riboflavin synthase
Source (natural)Organism: Aquifex aeolicus VF5 (bacteria)
Molecular weightTheoretical: 23.227842 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFTGLVEDLG KVKNLTLSSK GAKLSVETKL EDVKLGDSVS VNGACLTVVD IKSSTLTFDV SPETLKRTNL GKLKTGDYVN LERALRVGE RLGGHIVQGH VDFTAPVKSF NFLGEHYELV IEIPEEWSIY VVEKGSIALD GISLTVNYVK ENKVFINIIP H TYKSTNLQ ...String:
MFTGLVEDLG KVKNLTLSSK GAKLSVETKL EDVKLGDSVS VNGACLTVVD IKSSTLTFDV SPETLKRTNL GKLKTGDYVN LERALRVGE RLGGHIVQGH VDFTAPVKSF NFLGEHYELV IEIPEEWSIY VVEKGSIALD GISLTVNYVK ENKVFINIIP H TYKSTNLQ FKKVGDLLNV ETDILGKYVI NYLNKLKKKE DIFKEFLKW

UniProtKB: Riboflavin 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: 55 / Enantiomer: LEVO / EC number: 6,7-dimethyl-8-ribityllumazine synthase
Source (natural)Organism: Aquifex aeolicus VF5 (bacteria)
Molecular weightTheoretical: 18.126709 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MEIYEGKLTA EGLRFGIVAS RFNHALVDRL VEGAIDCIVR HGGREEDITL VRVPGSWEIP VAAGELARKE DIDAVIAIGV LIRGATPHF DYIASEVSKG LANLSLELRK PITFGVITAD TLEQAIERAG TKHGNKGWEA ALSAIEMANL FKSLRLEGGW S HPQFEK

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

Concentration0.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMNaPisodium phosphate
200.0 mMNaClsodium chloride
5.0 mMEDTAethylenediaminetetraacetic acid
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: GRAPHENE OXIDE / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 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: 8625 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.6 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: 1749455 / Details: 3D template picking
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 25459
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3) / Details: Ab initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3) / Details: Local Refinement
Final 3D classificationNumber classes: 3 / Avg.num./class: 25000 / Software - Name: cryoSPARC (ver. 4.5.3) / Details: 3D class with 4 A filter resolution and PCA
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

1hqk

source_name: PDB, initial_model_type: experimental modellumazine synthase
source_name: AlphaFold, initial_model_type: in silico modelriboflavin synthase
DetailsInitial fitting was done using ChimeraX. Flexible fitting was done using Isolde.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9ryk:
Aquifex aeolicus lumazine synthase 11-pentamer cage in complex with riboflavin synthase trimer

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