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- PDB-22xo: Cryo-EM structure of E.coli LrhA -

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Basic information

Entry
Database: PDB / ID: 22xo
TitleCryo-EM structure of E.coli LrhA
ComponentsProbable HTH-type transcriptional regulator LrhA
KeywordsTRANSCRIPTION / LysR-type / Flagellar biosynthesis / Transcriptional factor
Function / homology
Function and homology information


cis-regulatory region sequence-specific DNA binding / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of 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
Probable HTH-type transcriptional regulator LrhA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsNiu, B. / Kikkawa, M. / Jiang, X.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24KF0141 Japan
Japan Society for the Promotion of Science (JSPS)24K18106 Japan
CitationJournal: J Mol Biol / Year: 2026
Title: Oligomerization-Dependent Regulation of LrhA Controls Bacterial Flagellar Biosynthesis.
Authors: Baichun Niu / Masahide Kikkawa / Xuguang Jiang /
Abstract: LysR-type transcriptional regulators (LTTRs) are a diverse family of proteins that regulate various cellular processes, including motility in bacteria. In Escherichia coli, the LTTR LrhA represses ...LysR-type transcriptional regulators (LTTRs) are a diverse family of proteins that regulate various cellular processes, including motility in bacteria. In Escherichia coli, the LTTR LrhA represses flagellar biosynthesis by inhibiting the flhDC operon. However, the structural basis underlying this regulation has remained unclear. Here, we determined both a high-resolution crystal structure and a cryo-EM reconstruction of LrhA, revealing a predominant and stable tetrameric organization with pronounced structural variability in its effector-binding region. Structural and biochemical analyses demonstrate that mutations in these variable regions perturb the oligomeric equilibrium of LrhA, shifting the balance between tetrameric and dimeric species. This shift correlates with enhanced DNA binding affinity and stronger repression of the flhDC promoter. While ligand binding may similarly modulate LrhA activity, our data primarily support a model in which alterations in oligomeric state mediated by the variable regions regulate LrhA function. Together, these findings provide a structural framework for understanding how LrhA controls bacterial motility and offer broader insights into oligomerization-based regulation within the LTTR family.
History
DepositionJan 27, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable HTH-type transcriptional regulator LrhA
B: Probable HTH-type transcriptional regulator LrhA
C: Probable HTH-type transcriptional regulator LrhA
D: Probable HTH-type transcriptional regulator LrhA


Theoretical massNumber of molelcules
Total (without water)147,1924
Polymers147,1924
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Probable HTH-type transcriptional regulator LrhA


Mass: 36798.090 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lrhA, genR, b2289, JW2284 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P36771
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: Tetrameric complex of HTH-type transcriptional regulator LrhA
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.1388 MDa / Experimental value: YES
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (BL21)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
7UCSF ChimeraXmodel fitting
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 765839 / Symmetry type: POINT
RefinementHighest resolution: 2.72 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036406
ELECTRON MICROSCOPYf_angle_d0.6658762
ELECTRON MICROSCOPYf_dihedral_angle_d6.612907
ELECTRON MICROSCOPYf_chiral_restr0.0411026
ELECTRON MICROSCOPYf_plane_restr0.0061134

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