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- EMDB-51001: Circularly permuted lumazine synthase twisted tube with 28 Angstr... -

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Basic information

Entry
Database: EMDB / ID: EMD-51001
TitleCircularly permuted lumazine synthase twisted tube with 28 Angstrom gap between double strands
Map dataCombined half maps symmetrized and post-processed by DeepEMhancer with binary mask normalization mode using refinement mask.
Sample
  • Complex: Circularly permuted lumazine synthase twisted tube with 28 Angstrom gap between double strands
    • 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)
Methodhelical reconstruction / cryo EM / Resolution: 3.1 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_51001.png

Downloads & links

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Map

FileDownload / File: emd_51001.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCombined half maps symmetrized and post-processed by DeepEMhancer with binary mask normalization mode using refinement mask.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 440 pix.
= 372.24 Å		0.85 Å/pix.
x 440 pix.
= 372.24 Å		0.85 Å/pix.
x 440 pix.
= 372.24 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.846 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0024639755 - 2.1455846
Average (Standard dev.)0.014724666 (±0.095829934)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 372.24002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51001_msk_1.map
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Mask #2

Fileemd_51001_msk_2.map
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Additional map: Map combined from 2 independent halves. Not post-processed...

Fileemd_51001_additional_1.map
AnnotationMap combined from 2 independent halves. Not post-processed and not symmetrized map.
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Additional map: Combined half maps post-processed using sharpening B factor 102.5.

Fileemd_51001_additional_2.map
AnnotationCombined half maps post-processed using sharpening B factor 102.5.
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AxesZYX

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Additional map: Combined half maps symmetrized and post-processed using sharpening...

Fileemd_51001_additional_3.map
AnnotationCombined half maps symmetrized and post-processed using sharpening B factor 102.5.
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AxesZYX

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Additional map: Combined half maps symmetrized and post-processed using sharpening...

Fileemd_51001_additional_4.map
AnnotationCombined half maps symmetrized and post-processed using sharpening B factor 102.5.
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AxesZYX

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Half map: #1

Fileemd_51001_half_map_1.map
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Half map: #2

Fileemd_51001_half_map_2.map
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Sample components

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Entire : Circularly permuted lumazine synthase twisted tube with 28 Angstr...

EntireName: Circularly permuted lumazine synthase twisted tube with 28 Angstrom gap between double strands
Components
  • Complex: Circularly permuted lumazine synthase twisted tube with 28 Angstrom gap between double strands
    • Protein or peptide: 6,7-dimethyl-8-ribityllumazine synthase

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Supramolecule #1: Circularly permuted lumazine synthase twisted tube with 28 Angstr...

SupramoleculeName: Circularly permuted lumazine synthase twisted tube with 28 Angstrom gap between double strands
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Circularly permuted (119) variant of Aquifex aeolicus lumazine synthase with C37S and A85C mutations
Source (natural)Organism: Aquifex aeolicus VF5 (bacteria)
Molecular weightTheoretical: 600 kDa/nm

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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(119, C37S, A85C),cpAaLS(119, C37S, A85C) / Number of copies: 100 / Enantiomer: LEVO / EC number: 6,7-dimethyl-8-ribityllumazine synthase
Source (natural)Organism: Aquifex aeolicus VF5 (bacteria)
Molecular weightTheoretical: 17.465934 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTLEQAIERA GTKHGNKGWE AALSAIEMAN LFKSLRGTGG SGSSMEIYEG KLTAEGLRFG IVASRFNHAL VDRLVEGAID SIVRHGGRE EDITLVRVPG SWEIPVAAGE LARKEDIDAV IAIGVLIRGC TPHFDYIASE VSKGLANLSL ELRKPITFGV I TAD

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
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration1 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
50.0 mMTris-HCltris(hydroxymethyl)aminomethane
150.0 mMNaClsodium chloride
1.0 mMTCEPtris(2-carboxyethyl)phosphine
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 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 12746 / Average electron dose: 42.44 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: 1.5 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

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 24.5 Å
Applied symmetry - Helical parameters - Δ&Phi: 57.0 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Software - details: Homogenous Refinement / Number images used: 192310
Segment selectionNumber selected: 1620295 / Software - Name: cryoSPARC (ver. 4.4.1) / Details: Filament tracing
Startup modelType of model: INSILICO MODEL
In silico model: Cylinder with a 200/130 Angstrom outer/inner diameter.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1) / Details: Maximum Likelihood using Helical Refinement
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-9g3j:
Circularly permuted lumazine synthase twisted tube with 28 Angstrom gap between double strands

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