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

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Basic information

Entry
Database: PDB / ID: 9g3p
TitleCircularly permuted lumazine synthase 12-pentamer spherical cage
Components6,7-dimethyl-8-ribityllumazine synthase
KeywordsDE NOVO PROTEIN / protein cage / protein engineering / self-assembly / geometry / helical reconstruction / bionanotechnology / polymorphism / pentamer
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 speciesAquifex aeolicus VF5 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.08 Å
AuthorsKoziej, L. / Azuma, Y.
Funding support Poland, European Union, 3items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.1Mar 19, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6,7-dimethyl-8-ribityllumazine synthase
B: 6,7-dimethyl-8-ribityllumazine synthase
C: 6,7-dimethyl-8-ribityllumazine synthase
D: 6,7-dimethyl-8-ribityllumazine synthase
E: 6,7-dimethyl-8-ribityllumazine synthase
F: 6,7-dimethyl-8-ribityllumazine synthase
G: 6,7-dimethyl-8-ribityllumazine synthase
H: 6,7-dimethyl-8-ribityllumazine synthase
I: 6,7-dimethyl-8-ribityllumazine synthase
J: 6,7-dimethyl-8-ribityllumazine synthase
K: 6,7-dimethyl-8-ribityllumazine synthase
L: 6,7-dimethyl-8-ribityllumazine synthase
M: 6,7-dimethyl-8-ribityllumazine synthase
N: 6,7-dimethyl-8-ribityllumazine synthase
O: 6,7-dimethyl-8-ribityllumazine synthase
P: 6,7-dimethyl-8-ribityllumazine synthase
Q: 6,7-dimethyl-8-ribityllumazine synthase
R: 6,7-dimethyl-8-ribityllumazine synthase
S: 6,7-dimethyl-8-ribityllumazine synthase
T: 6,7-dimethyl-8-ribityllumazine synthase
U: 6,7-dimethyl-8-ribityllumazine synthase
V: 6,7-dimethyl-8-ribityllumazine synthase
W: 6,7-dimethyl-8-ribityllumazine synthase
X: 6,7-dimethyl-8-ribityllumazine synthase
Y: 6,7-dimethyl-8-ribityllumazine synthase
Z: 6,7-dimethyl-8-ribityllumazine synthase
AA: 6,7-dimethyl-8-ribityllumazine synthase
BA: 6,7-dimethyl-8-ribityllumazine synthase
CA: 6,7-dimethyl-8-ribityllumazine synthase
DA: 6,7-dimethyl-8-ribityllumazine synthase
EA: 6,7-dimethyl-8-ribityllumazine synthase
FA: 6,7-dimethyl-8-ribityllumazine synthase
GA: 6,7-dimethyl-8-ribityllumazine synthase
HA: 6,7-dimethyl-8-ribityllumazine synthase
IA: 6,7-dimethyl-8-ribityllumazine synthase
JA: 6,7-dimethyl-8-ribityllumazine synthase
KA: 6,7-dimethyl-8-ribityllumazine synthase
LA: 6,7-dimethyl-8-ribityllumazine synthase
MA: 6,7-dimethyl-8-ribityllumazine synthase
NA: 6,7-dimethyl-8-ribityllumazine synthase
OA: 6,7-dimethyl-8-ribityllumazine synthase
PA: 6,7-dimethyl-8-ribityllumazine synthase
QA: 6,7-dimethyl-8-ribityllumazine synthase
RA: 6,7-dimethyl-8-ribityllumazine synthase
SA: 6,7-dimethyl-8-ribityllumazine synthase
TA: 6,7-dimethyl-8-ribityllumazine synthase
UA: 6,7-dimethyl-8-ribityllumazine synthase
VA: 6,7-dimethyl-8-ribityllumazine synthase
WA: 6,7-dimethyl-8-ribityllumazine synthase
XA: 6,7-dimethyl-8-ribityllumazine synthase
YA: 6,7-dimethyl-8-ribityllumazine synthase
ZA: 6,7-dimethyl-8-ribityllumazine synthase
AB: 6,7-dimethyl-8-ribityllumazine synthase
BB: 6,7-dimethyl-8-ribityllumazine synthase
CB: 6,7-dimethyl-8-ribityllumazine synthase
DB: 6,7-dimethyl-8-ribityllumazine synthase
EB: 6,7-dimethyl-8-ribityllumazine synthase
FB: 6,7-dimethyl-8-ribityllumazine synthase
GB: 6,7-dimethyl-8-ribityllumazine synthase
HB: 6,7-dimethyl-8-ribityllumazine synthase


Theoretical massNumber of molelcules
Total (without water)1,046,99660
Polymers1,046,99660
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
6,7-dimethyl-8-ribityllumazine synthase / DMRL synthase / LS / Lumazine synthase


Mass: 17449.938 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Details: cpAaLS(84),cpAaLS(84) / Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: ribH, aq_132 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)
References: UniProt: O66529, 6,7-dimethyl-8-ribityllumazine synthase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Circularly permuted lumazine synthase 12-pentamer spherical cage
Type: COMPLEX
Details: Circularly permuted (84) variant of Aquifex aeolicus lumazine synthase
Entity ID: all / Source: RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
111 MDaYES
21NO
Source (natural)Organism: Aquifex aeolicus VF5 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21-Gold(DE3)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMtris(hydroxymethyl)aminomethaneTris-HCl1
2150 mMsodium chlorideNaCl1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 105000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8486
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2EPU2.10.0.1941RELimage acquisition
4RELION3.1CTF correction
7UCSF ChimeraX1.7model fitting
8ISOLDE1.7model fitting
10PHENIX1.20.1-4487model refinement
11RELION3.1initial Euler assignment
12RELION3.1final Euler assignment
13RELION3.1classification
14RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 590975 / Details: Template picking
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98492 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: Initial fitting was done using ChimeraX. Flexible fitting was done using Isolde.
Atomic model buildingPDB-ID: 1HQK

1hqk


Accession code: 1HQK / Source name: PDB / Type: experimental model

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