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- EMDB-55156: Cryo-EM structure of Mlc in complex with ptsG operator DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-55156
TitleCryo-EM structure of Mlc in complex with ptsG operator DNA
Map dataComposite map
Sample
  • Complex: Tetrameric Mlc in complex with ptsG operator dsDNA
    • Protein or peptide: DNA-binding transcriptional repressor Mlc
    • DNA: DNA (27-MER)
    • DNA: DNA (27-MER)
  • Ligand: ZINC ION
KeywordsRepressor / DNA-binding protein / transcription regulation / gene regulation / carbohydrate utilization / metal-binding / DNA / operator / DNA BINDING PROTEIN
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA-templated transcription / DNA binding / membrane / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
ROK family / ROK family / ATPase, nucleotide binding domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA-binding transcriptional repressor Mlc
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.47 Å
AuthorsRoth P / Fotiadis D
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation10001444 Switzerland
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis of Mlc-mediated transcriptional regulation of carbohydrate metabolism.
Authors: Patrick Roth / Inken Fender / Jean-Marc Jeckelmann / Zöhre Ucurum / Thomas Lemmin / Dimitrios Fotiadis /
Abstract: The global transcriptional repressor Mlc of Escherichia coli regulates genes involved in carbohydrate transport and metabolism, particularly glucose uptake via the glucose-specific phosphotransferase ...The global transcriptional repressor Mlc of Escherichia coli regulates genes involved in carbohydrate transport and metabolism, particularly glucose uptake via the glucose-specific phosphotransferase system (PTS). Unlike conventional repressors, Mlc exemplifies a system in which interactions with diverse macromolecules govern its activity. Here, we present cryo-electron microscopy structures of Mlc alone and in complexes with regulatory partners, including the glucose-specific PTS transporter IICB, a cognate DNA operator and the anti-repressor MtfA, capturing multiple assemblies central to transcription control. These structures reveal the molecular architecture of Mlc and its interactions with binding partners. Together with molecular dynamics simulations, they provide insights into the structural dynamics of these complexes. Our findings establish the structural basis of membrane-transporter involvement in transcriptional regulation, the mechanism of anti-repressor action and DNA recognition. This work provides a structural framework for understanding bacterial transcriptional regulation across diverse systems.
History
DepositionSep 25, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55156.png

Downloads & links

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Map

FileReleased
AnnotationComposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 320 pix.
= 300.032 Å		0.94 Å/pix.
x 320 pix.
= 300.032 Å		0.94 Å/pix.
x 320 pix.
= 300.032 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9376 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.10462068 - 1.9313045
Average (Standard dev.)0.001019108 (±0.021322383)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 300.032 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Tetrameric Mlc in complex with ptsG operator dsDNA

EntireName: Tetrameric Mlc in complex with ptsG operator dsDNA
Components
  • Complex: Tetrameric Mlc in complex with ptsG operator dsDNA
    • Protein or peptide: DNA-binding transcriptional repressor Mlc
    • DNA: DNA (27-MER)
    • DNA: DNA (27-MER)
  • Ligand: ZINC ION

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Supramolecule #1: Tetrameric Mlc in complex with ptsG operator dsDNA

SupramoleculeName: Tetrameric Mlc in complex with ptsG operator dsDNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: DNA-binding transcriptional repressor Mlc

MacromoleculeName: DNA-binding transcriptional repressor Mlc / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 49.902996 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGGSHHHHHH GMASMTGGQQ MGRDLYDDDD KDRWGSELEV LFQGPKLMVA ENQPGHIDQI KQTNAGAVYR LIDQLGPVSR IDLSRLAQL APASITKIVR EMLEAHLVQE LEIKEAGNRG RPAVGLVVET EAWHYLSLRI SRGEIFLALR DLSSKLVVEE S QELALKDD ...String:
MGGSHHHHHH GMASMTGGQQ MGRDLYDDDD KDRWGSELEV LFQGPKLMVA ENQPGHIDQI KQTNAGAVYR LIDQLGPVSR IDLSRLAQL APASITKIVR EMLEAHLVQE LEIKEAGNRG RPAVGLVVET EAWHYLSLRI SRGEIFLALR DLSSKLVVEE S QELALKDD LPLLDRIISH IDQFFIRHQK KLERLTSIAI TLPGIIDTEN GIVHRMPFYE DVKEMPLGEA LEQHTGVPVY IQ HDISAWT MAEALFGASR GARDVIQVVI DHNVGAGVIT DGHLLHAGSS SLVEIGHTQV DPYGKRCYCG NHGCLETIAS VDS ILELAQ LRLNQSMSSM LHGQPLTVDS LCQAALRGDL LAKDIITGVG AHVGRILAIM VNLFNPQKIL IGSPLSKAAD ILFP VISDS IRQQALPAYS QHISVESTQF SNQGTMAGAA LVKDAMYNGS LLIRLLQGLE

UniProtKB: DNA-binding transcriptional repressor Mlc

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Macromolecule #2: DNA (27-MER)

MacromoleculeName: DNA (27-MER) / type: dna / ID: 2 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 8.889796 KDa
SequenceString:
(DT)(DT)(DT)(DA)(DT)(DT)(DT)(DA)(DT)(DT) (DA)(DC)(DA)(DC)(DA)(DG)(DA)(DG)(DT)(DA) (DA)(DA)(DA)(DT)(DA)(DA)(DT)(DT)(DC)

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Macromolecule #3: DNA (27-MER)

MacromoleculeName: DNA (27-MER) / type: dna / ID: 3 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 8.929818 KDa
SequenceString:
(DG)(DA)(DA)(DT)(DT)(DA)(DT)(DT)(DT)(DT) (DA)(DC)(DT)(DC)(DT)(DG)(DT)(DG)(DT)(DA) (DA)(DT)(DA)(DA)(DA)(DT)(DA)(DA)(DA)

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration0.8 mg/mL
BufferpH: 8
Details: 20 mM HEPES-NaOH pH 8.0, 150 mM NaCl, 1 mM b-ME, 1 mM MgCl2, 50 uM ZnCl2
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 10993 / Average exposure time: 3.51 sec. / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 322270
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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