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- EMDB-68756: Cryo-EM structure of E.coli LrhA -

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Basic information

Entry
Database: EMDB / ID: EMD-68756
TitleCryo-EM structure of E.coli LrhA
Map data
Sample
  • Complex: Tetrameric complex of HTH-type transcriptional regulator LrhA
    • Protein or peptide: Probable HTH-type transcriptional regulator LrhA
KeywordsLysR-type / Flagellar biosynthesis / Transcriptional factor / TRANSCRIPTION
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsNiu B / Kikkawa M / Jiang X
Funding support Japan, 2 items
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, 2026-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_68756.png

Downloads & links

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Map

FileDownload / File: emd_68756.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 192 pix.
= 197.76 Å		1.03 Å/pix.
x 192 pix.
= 197.76 Å		1.03 Å/pix.
x 192 pix.
= 197.76 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.02296359 - 2.0373237
Average (Standard dev.)0.0016231725 (±0.028598055)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 197.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_68756_msk_1.map
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Additional map: #1

Fileemd_68756_additional_1.map
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Half map: #1

Fileemd_68756_half_map_1.map
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Half map: #2

Fileemd_68756_half_map_2.map
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Sample components

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Entire : Tetrameric complex of HTH-type transcriptional regulator LrhA

EntireName: Tetrameric complex of HTH-type transcriptional regulator LrhA
Components
  • Complex: Tetrameric complex of HTH-type transcriptional regulator LrhA
    • Protein or peptide: Probable HTH-type transcriptional regulator LrhA

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Supramolecule #1: Tetrameric complex of HTH-type transcriptional regulator LrhA

SupramoleculeName: Tetrameric complex of HTH-type transcriptional regulator LrhA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 138.8 KDa

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Macromolecule #1: Probable HTH-type transcriptional regulator LrhA

MacromoleculeName: Probable HTH-type transcriptional regulator LrhA / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 36.79809 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MISANRPIIN LDLDLLRTFV AVADLNTFAA AAAAVCRTQS AVSQQMQRLE QLVGKELFAR HGRNKLLTE HGIQLLGYAR KILRFNDEAC SSLMFSNLQG VLTIGASDES ADTILPFLLN RVSSVYPKLA LDVRVKRNAY M AEMLESQE ...String:
MGSSHHHHHH SSGLVPRGSH MISANRPIIN LDLDLLRTFV AVADLNTFAA AAAAVCRTQS AVSQQMQRLE QLVGKELFAR HGRNKLLTE HGIQLLGYAR KILRFNDEAC SSLMFSNLQG VLTIGASDES ADTILPFLLN RVSSVYPKLA LDVRVKRNAY M AEMLESQE VDLMVTTHRP SAFKALNLRT SPTHWYCAAE YILQKGEPIP LVLLDDPSPF RDMVLATLNK ADIPWRLAYV AS TLPAVRA AVKAGLGVTA RPVEMMSPDL RVLSGVDGLP PLPDTEYLLC YDPSSNNELA QVIYQAMESY HNPWQYSPMS APE GDDSLL IERDIE

UniProtKB: Probable HTH-type transcriptional regulator LrhA

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 765839
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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