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- EMDB-39478: Structure of Aquifex aeolicus Lumazine Synthase by Cryo-Electron ... -

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Basic information

Entry
Database: EMDB / ID: EMD-39478
TitleStructure of Aquifex aeolicus Lumazine Synthase by Cryo-Electron Microscopy to 1.42 Angstrom Resolution
Map dataPost processed map
Sample
  • Complex: Aquifex aeolicus Lumazine Synthase
    • Protein or peptide: Lumazine synthase
KeywordsEnzyme involved in riboflavin biosynthesis / BIOSYNTHETIC 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
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 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.42 Å
AuthorsSavva CG / Sobhy M / De Biasio A / Hamdan SM
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Atomic Resolution structure of Aquifex aeolicus Lumazine Synthase by Cryo-Electron Microscopy
Authors: Savva CG / Sobhy M / De Biasio A / Hamdan SM
History
DepositionMar 16, 2024-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39478.png

Downloads & links

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Map

FileDownload / File: emd_39478.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost processed map
Voxel sizeX=Y=Z: 0.4553 Å
Density
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.16591452 - 0.34502378
Average (Standard dev.)0.000018229632 (±0.0066114715)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions700700700
Spacing700700700
CellA=B=C: 318.71 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39478_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_39478_half_map_1.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 1

Fileemd_39478_half_map_2.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Aquifex aeolicus Lumazine Synthase

EntireName: Aquifex aeolicus Lumazine Synthase
Components
  • Complex: Aquifex aeolicus Lumazine Synthase
    • Protein or peptide: Lumazine synthase

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Supramolecule #1: Aquifex aeolicus Lumazine Synthase

SupramoleculeName: Aquifex aeolicus Lumazine Synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Aquifex aeolicus (bacteria)
Molecular weightTheoretical: 1.065 MDa

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Macromolecule #1: Lumazine synthase

MacromoleculeName: Lumazine synthase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Aquifex aeolicus (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MQIYEGKLTA EGLRFGIVAS RFNHALVDRL VEGAIDCIVR HGGREEDITL VRVPGSWEIP VAAGELARK EDIDAVIAIG VLIRGATPHF DYIASEVSKG LANLSLELRK PITFGVITAD T LEQAIERA GTKHGNKGWE AALSAIEMAN LFKSLRWSHP QFEK

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

Concentration2.75 mg/mL
BufferpH: 7.5 / Details: 20mM Tris pH 7.5, 150mM NaCl and 1mM DTT
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: 30 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot time: 3 sec Wait time: 0 sec.
DetailsIn buffer 20mM Tris pH 7.5, 150mM NaCl and 1mM DTT

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 12657 / Average exposure time: 3.0 sec. / Average electron dose: 46.0 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: 1.2 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 165000
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: 698248
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 1.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 470878
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT
Output model

PDB-8yt4:
Structure of Aquifex aeolicus Lumazine Synthase by Cryo-Electron Microscopy to 1.42 Angstrom Resolution

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