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- EMDB-52168: LysR Type Transcriptional Regulator LsrB from Agrobacterium tumef... -

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Basic information

Entry
Database: EMDB / ID: EMD-52168
TitleLysR Type Transcriptional Regulator LsrB from Agrobacterium tumefaciens
Map dataSharpened Map of the Lsrb-SBD Dimer from non-uniform refinement in Cryosparc
Sample
  • Organelle or cellular component: Dimeric LTTR-type transcriptional regulator LsrB
    • Protein or peptide: Transcriptional regulator, LysR family
KeywordsLysR-type trancriptional regulator / DNA-Binding / Agrobacterium / transcription factor / DNA BINDING PROTEIN
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcriptional regulator, LysR family
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria) / Agrobacterium fabrum str. C58 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsElders H / Schmidt JJ / Fiedler R / Hofmann E / Narberhaus F
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)NA 240/11-2 Germany
German Research Foundation (DFG)Research Training Group 2341 Germany
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Two redox-responsive LysR-type transcription factors control the oxidative stress response of Agrobacterium tumefaciens.
Authors: Janka J Schmidt / Vivian B Brandenburg / Hannah Elders / Saba Shahzad / Sina Schäkermann / Ronja Fiedler / Lisa R Knoke / Yvonne Pfänder / Pascal Dietze / Hannah Bille / Bela Gärtner / ...Authors: Janka J Schmidt / Vivian B Brandenburg / Hannah Elders / Saba Shahzad / Sina Schäkermann / Ronja Fiedler / Lisa R Knoke / Yvonne Pfänder / Pascal Dietze / Hannah Bille / Bela Gärtner / Lennart J Albin / Lars I Leichert / Julia E Bandow / Eckhard Hofmann / Franz Narberhaus /
Abstract: Pathogenic bacteria often encounter fluctuating reactive oxygen species (ROS) levels, particularly during host infection, necessitating robust redox-sensing mechanisms for survival. The LysR-type ...Pathogenic bacteria often encounter fluctuating reactive oxygen species (ROS) levels, particularly during host infection, necessitating robust redox-sensing mechanisms for survival. The LysR-type transcriptional regulator (LTTR) OxyR is a widely conserved bacterial thiol-based redox sensor. However, members of the Rhizobiales also encode LsrB, a second LTTR with potential redox-sensing function. This study explores the roles of OxyR and LsrB in the plant-pathogen Agrobacterium tumefaciens. Through single and combined deletions, we observed increased H2O2 sensitivity, underscoring their function in oxidative defense. Genome-wide transcriptome profiling under H2O2 exposure revealed that OxyR and LsrB co-regulate key antioxidant genes, including katG, encoding a bifunctional catalase/peroxidase. Agrobacterium tumefaciens LsrB possesses four cysteine residues potentially involved in redox sensing. To elucidate the structural basis for redox-sensing, we applied single-particle cryo-EM (cryogenic electron microscopy) to experimentally confirm an AlphaFold model of LsrB, identifying two proximal cysteine pairs. In vitro thiol-trapping coupled with mass spectrometry confirmed reversible thiol modifications of all four residues, suggesting a functional role in redox regulation. Collectively, these findings reveal that A. tumefaciens employs two cysteine-based redox sensing transcription factors, OxyR and LsrB, to withstand oxidative stress encountered in host and soil environments.
History
DepositionNov 20, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52168.png

Downloads & links

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Map

FileDownload / File: emd_52168.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened Map of the Lsrb-SBD Dimer from non-uniform refinement in Cryosparc
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 200 pix.
= 164. Å		0.82 Å/pix.
x 200 pix.
= 164. Å		0.82 Å/pix.
x 200 pix.
= 164. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.75
Minimum - Maximum-2.7731833 - 3.3499846
Average (Standard dev.)-0.00087680464 (±0.11227393)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 164.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Halfmap A from non-uniform refinement in Cryosparc

Fileemd_52168_half_map_1.map
AnnotationHalfmap A from non-uniform refinement in Cryosparc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap B from non-uniform refinement in Cryosparc

Fileemd_52168_half_map_2.map
AnnotationHalfmap B from non-uniform refinement in Cryosparc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dimeric LTTR-type transcriptional regulator LsrB

EntireName: Dimeric LTTR-type transcriptional regulator LsrB
Components
  • Organelle or cellular component: Dimeric LTTR-type transcriptional regulator LsrB
    • Protein or peptide: Transcriptional regulator, LysR family

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Supramolecule #1: Dimeric LTTR-type transcriptional regulator LsrB

SupramoleculeName: Dimeric LTTR-type transcriptional regulator LsrB / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Agrobacterium tumefaciens (bacteria)
Molecular weightTheoretical: 76 KDa

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Macromolecule #1: Transcriptional regulator, LysR family

MacromoleculeName: Transcriptional regulator, LysR family / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium fabrum str. C58 (bacteria)
Molecular weightTheoretical: 35.374312 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAMPLDWDKL RIFHAAAEAG SFTHAADKLH LSQSAISRQV SALEQDVGVK LFHRHARGLI LTEQGELLYR TAHDVLLKLE TVKMQLTET TEKPSGKLRV TTTVGLGQGW LTDKVQEFLQ LYPEMSIQLI LDNEELDVNM RHADCAIRLR QPQQSDLIQR K LFTVHMHV ...String:
MAMPLDWDKL RIFHAAAEAG SFTHAADKLH LSQSAISRQV SALEQDVGVK LFHRHARGLI LTEQGELLYR TAHDVLLKLE TVKMQLTET TEKPSGKLRV TTTVGLGQGW LTDKVQEFLQ LYPEMSIQLI LDNEELDVNM RHADCAIRLR QPQQSDLIQR K LFTVHMHV YAAPSYINRH GEPQSVEDLD NHRIISFGEP APNYLLDVNW LENAGRSSDN TRIPHLQINS QTSIKRACLL GI GIACLPD YIVGRDPGLI QLSLAADIPS FDTYFCYPDE MKNAAKLKAF RDFIVAKARN WNFGTSAWSH PQFEK

UniProtKB: Transcriptional regulator, LysR family

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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

Concentration1.2 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Pressure: 4.0 kPa / Details: 15mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Detailshomogeneous dimeric sample

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 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

Particle selectionNumber selected: 8864865
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold 3 model of LsrB SBD dimer
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 484971
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final 3D classificationNumber classes: 3 / Avg.num./class: 500000 / Software - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9hh1:
LysR Type Transcriptional Regulator LsrB from Agrobacterium tumefaciens

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