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- EMDB-50071: Cryo-EM structure of the icosahedral lumazine synthase from Vicia... -

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Basic information

Entry
Database: EMDB / ID: EMD-50071
TitleCryo-EM structure of the icosahedral lumazine synthase from Vicia faba.
Map dataSharpened map (from RELION Postprocess)
Sample
  • Complex: Icosahedral 60-mer
    • Protein or peptide: 6,7-dimethyl-8-ribityllumazine synthase
Keywordsicosahedral enzyme / TRANSFERASE
Function / homology6,7-dimethyl-8-ribityllumazine synthase / 6,7-dimethyl-8-ribityllumazine synthase activity / Lumazine synthase / riboflavin synthase complex / Lumazine/riboflavin synthase / Lumazine/riboflavin synthase superfamily / 6,7-dimethyl-8-ribityllumazine synthase / riboflavin biosynthetic process / 6,7-dimethyl-8-ribityllumazine synthase
Function and homology information
Biological speciesVicia faba (fava bean)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsChee M / Trapani S / Hoh F / Lai Kee Him J / Yvon M / Blanc S / Bron P
Funding support France, 1 items
OrganizationGrant numberCountry
Montpellier University of Excellence (MUSE)BLANC-MUSE2020-Multivir France
CitationJournal: To Be Published
Title: Cryo-EM structure of the icosahedral lumazine synthase from Vicia faba.
Authors: Chee M / Trapani S / Hoh F / Lai Kee Him J / Yvon M / Blanc S / Bron P
History
DepositionApr 11, 2024-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50071.png

Downloads & links

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Map

FileDownload / File: emd_50071.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map (from RELION Postprocess)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.26 Å/pix.
x 320 pix.
= 404. Å		1.26 Å/pix.
x 320 pix.
= 404. Å		1.26 Å/pix.
x 320 pix.
= 404. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2625 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.081949815 - 0.14827992
Average (Standard dev.)0.00016632328 (±0.0062443144)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 404.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50071_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_50071_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50071_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_50071_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 : Icosahedral 60-mer

EntireName: Icosahedral 60-mer
Components
  • Complex: Icosahedral 60-mer
    • Protein or peptide: 6,7-dimethyl-8-ribityllumazine synthase

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Supramolecule #1: Icosahedral 60-mer

SupramoleculeName: Icosahedral 60-mer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vicia faba (fava bean)
Molecular weightTheoretical: 1.45 MDa

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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: 1 / Enantiomer: LEVO / EC number: 6,7-dimethyl-8-ribityllumazine synthase
Source (natural)Organism: Vicia faba (fava bean)
Molecular weightTheoretical: 16.505764 KDa
SequenceString:
AVRHLTGSVT RTQGLRFAVV VARFNEIITR PLLEGALGTF KNYSVQDEDI DVVWVPGCFE IGAVATRLGK SGKYHAIICI GAVIRGDTT HYDAVANSAA SGVLSAGLNS GVPCIFGVLT CEDMDQAINR AGGKSGNKGA EAALTAIEMA SLFEHHLQ

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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 7.34 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.0) / Number images used: 64092
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.0)
Final 3D classificationSoftware - Name: RELION (ver. 4.0.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: other / Details: poly-Ala model manually built using Coot
Output model

PDB-9ez8:
Cryo-EM structure of the icosahedral lumazine synthase from Vicia faba.

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