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- EMDB-42072: Cryo-EM Structure of Brucella Abortus Lumazine Synthase (BLS) Eng... -

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Basic information

Entry
Database: EMDB / ID: EMD-42072
TitleCryo-EM Structure of Brucella Abortus Lumazine Synthase (BLS) Engineered with Shiga Toxin I subunit B (Stx1B)
Map datatructure of Brucella Abortus Lumazine Synthase (BLS) Engineered with Shiga Toxin I subunit B (Stx1B)
Sample
  • Complex: Chimeric BLS-Stx1B protein
    • Protein or peptide: Shiga toxin subunit B,6,7-dimethyl-8-ribityllumazine synthase 2
KeywordsCHIMERA / SHIGA / TOXIN / IMMUNOGEN
Function / homology
Function and homology information


symbiont-mediated hemolysis of host erythrocyte / 6,7-dimethyl-8-ribityllumazine synthase / 6,7-dimethyl-8-ribityllumazine synthase activity / riboflavin synthase complex / riboflavin biosynthetic process / toxin activity / extracellular region / cytosol
Similarity search - Function
Shiga-like toxin, beta subunit / Shiga-like toxin beta subunit / Lumazine synthase / Lumazine/riboflavin synthase / Lumazine/riboflavin synthase superfamily / 6,7-dimethyl-8-ribityllumazine synthase / Enterotoxin
Similarity search - Domain/homology
6,7-dimethyl-8-ribityllumazine synthase 2 / Shiga toxin 1 B subunit
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria) / Brucella abortus biovar 1 (strain 9-941)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.37 Å
AuthorsCristofalo AE / Sharma A / Cerutti ML / Sharma K / Zylberman V / Goldbaum FA / Borgnia MJ / Otero LH
Funding support Argentina, United States, 2 items
OrganizationGrant numberCountry
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT 2020-3047 Argentina
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIC ES103326 United States
CitationJournal: To Be Published
Title: Cryo-EM Structure of Brucella Abortus Lumazine Synthase (BLS) Engineered with Shiga Toxin I subunit B (Stx1B)
Authors: Cristofalo AE / Sharma A / Cerutti ML / Sharma K / Zylberman V / Goldbaum FA / Borgnia MJ / Otero LH
History
DepositionSep 22, 2023-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42072.png

Downloads & links

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Map

FileDownload / File: emd_42072.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationtructure of Brucella Abortus Lumazine Synthase (BLS) Engineered with Shiga Toxin I subunit B (Stx1B)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.66 Å/pix.
x 480 pix.
= 316.8 Å		0.66 Å/pix.
x 480 pix.
= 316.8 Å		0.66 Å/pix.
x 480 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.4
Minimum - Maximum-12.529885 - 38.275481999999997
Average (Standard dev.)0.000000000532266 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 316.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map 1

Fileemd_42072_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_42072_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Chimeric BLS-Stx1B protein

EntireName: Chimeric BLS-Stx1B protein
Components
  • Complex: Chimeric BLS-Stx1B protein
    • Protein or peptide: Shiga toxin subunit B,6,7-dimethyl-8-ribityllumazine synthase 2

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Supramolecule #1: Chimeric BLS-Stx1B protein

SupramoleculeName: Chimeric BLS-Stx1B protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Engineered chimera of Brucella abortus Lumazine Synthase (BLS) and Shiga Toxin 1 subunit B (Stx1B)
Source (natural)Organism: Escherichia coli O157:H7 (bacteria) / Location in cell: extracellular region

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Macromolecule #1: Shiga toxin subunit B,6,7-dimethyl-8-ribityllumazine synthase 2

MacromoleculeName: Shiga toxin subunit B,6,7-dimethyl-8-ribityllumazine synthase 2
type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO / EC number: 6,7-dimethyl-8-ribityllumazine synthase
Source (natural)Organism: Brucella abortus biovar 1 (strain 9-941)
Molecular weightTheoretical: 25.39083 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MHTPDCVTGK VEYTKYNDDD TFTVKVGDKE LFTNRWNLQS LLLSAQITGM TVTIKTNACH NGGGFSEVIF RGSGSGSGSG SLKTSFKIA FIQARWHADI VDEARKSFVA ELAAKTGGSV EVEIFDVPGA YEIPLHAKTL ARTGRYAAIV GAAFVIDGGI Y RHDFVATA ...String:
MHTPDCVTGK VEYTKYNDDD TFTVKVGDKE LFTNRWNLQS LLLSAQITGM TVTIKTNACH NGGGFSEVIF RGSGSGSGSG SLKTSFKIA FIQARWHADI VDEARKSFVA ELAAKTGGSV EVEIFDVPGA YEIPLHAKTL ARTGRYAAIV GAAFVIDGGI Y RHDFVATA VINGMMQVQL ETEVPVLSVV LTPHHFHESK EHHDFFHAHF KVKGVEAAHA ALQIVSERSR IAALV

UniProtKB: Shiga toxin 1 B subunit, 6,7-dimethyl-8-ribityllumazine synthase 2

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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

Concentration1.4 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClsodium chloride
2.7 mMKClpotassium chloride
10.0 mMNa2HPO4sodium hydrogen phosphate
1.8 mMKH2PO4potassium dihydrogen phosphate
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
DetailsPreliminary grid screening was performed using SmartScope software
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 5884 / Average electron dose: 65.0 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: 2.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000
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: 1773142
Startup modelType of model: NONE / Details: Ab-initio model was generated
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 88636
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1) / Software - details: Ab-initio job was used
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1) / Software - details: Homogeneous refinement job was used
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.2.1)

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Atomic model buiding 1

Initial model
PDB IDChain

1xn1

source_name: PDB, initial_model_type: experimental model

1qnu

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8uav:
Cryo-EM Structure of Brucella Abortus Lumazine Synthase (BLS) Engineered with Shiga Toxin I subunit B (Stx1B)

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