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- EMDB-55165: Cryo-EM structure of the Mlc repressor in complex with the glucos... -

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Basic information

Entry
Database: EMDB / ID: EMD-55165
TitleCryo-EM structure of the Mlc repressor in complex with the glucose-specific IICB transporter
Map dataComposite reconstruction
Sample
  • Complex: Mlc tetramer in complex with the dimeric glucose-specific IICB transporter
    • Protein or peptide: PTS system glucose-specific EIICB component
    • Protein or peptide: DNA-binding transcriptional repressor Mlc
  • Ligand: beta-D-glucopyranose
  • Ligand: ZINC ION
KeywordsRepressor / DNA-binding protein / transcription regulation / gene regulation / carbohydrate utilization / metal-binding / membrane transporter / glucose / transmembrane protein / membrane-tethering / DNA BINDING PROTEIN
Function / homology
Function and homology information


protein-phosphocysteine-glucose phosphotransferase system transporter activity / protein-Npi-phosphohistidine-D-glucose phosphotransferase / protein-N(PI)-phosphohistidine-carbohydrate phosphotransferase activity / D-glucose transmembrane transporter activity / D-glucose import across plasma membrane / D-glucose transmembrane transport / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / regulation of DNA-templated transcription / DNA-templated transcription ...protein-phosphocysteine-glucose phosphotransferase system transporter activity / protein-Npi-phosphohistidine-D-glucose phosphotransferase / protein-N(PI)-phosphohistidine-carbohydrate phosphotransferase activity / D-glucose transmembrane transporter activity / D-glucose import across plasma membrane / D-glucose transmembrane transport / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / regulation of DNA-templated transcription / DNA-templated transcription / DNA binding / membrane / metal ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Phosphotransferase system, maltose/glucose-specific subfamily IIC component / PTS system glucose-specific IIBC component / : / Phosphotransferase system, IIB component, type 1 / Phosphotransferase system, EIIC component, type 1 / Phosphotransferase system EIIB, cysteine phosphorylation site / Glucose permease domain IIB / phosphotransferase system, EIIB / PTS EIIB domains cysteine phosphorylation site signature. / PTS_EIIB type-1 domain profile. ...Phosphotransferase system, maltose/glucose-specific subfamily IIC component / PTS system glucose-specific IIBC component / : / Phosphotransferase system, IIB component, type 1 / Phosphotransferase system, EIIC component, type 1 / Phosphotransferase system EIIB, cysteine phosphorylation site / Glucose permease domain IIB / phosphotransferase system, EIIB / PTS EIIB domains cysteine phosphorylation site signature. / PTS_EIIB type-1 domain profile. / PTS_EIIC type-1 domain profile. / Phosphotransferase system, EIIC / Phosphotransferase system, EIIC / 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 / PTS system glucose-specific EIICB component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 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_55165.png

Downloads & links

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Map

FileReleased
AnnotationComposite reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 320 pix.
= 394.56 Å		1.23 Å/pix.
x 320 pix.
= 394.56 Å		1.23 Å/pix.
x 320 pix.
= 394.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.233 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.05890184 - 2.4890559
Average (Standard dev.)0.00086171203 (±0.019274712)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 394.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Mlc tetramer in complex with the dimeric glucose-specific IICB tr...

EntireName: Mlc tetramer in complex with the dimeric glucose-specific IICB transporter
Components
  • Complex: Mlc tetramer in complex with the dimeric glucose-specific IICB transporter
    • Protein or peptide: PTS system glucose-specific EIICB component
    • Protein or peptide: DNA-binding transcriptional repressor Mlc
  • Ligand: beta-D-glucopyranose
  • Ligand: ZINC ION

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Supramolecule #1: Mlc tetramer in complex with the dimeric glucose-specific IICB tr...

SupramoleculeName: Mlc tetramer in complex with the dimeric glucose-specific IICB transporter
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: PTS system glucose-specific EIICB component

MacromoleculeName: PTS system glucose-specific EIICB component / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
EC number: protein-Npi-phosphohistidine-D-glucose phosphotransferase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 50.719223 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFKNAFANLQ KVGKSLMLPV SVLPIAGILL GVGSANFSWL PAVVSHVMAE AGGSVFANMP LIFAIGVALG FTNNDGVSAL AAVVAYGIM VKTMAVVAPL VLHLPAEEIA SKHLADTGVL GGIISGAIAA YMFNRFYRIK LPEYLGFFAG KRFVPIISGL A AIFTGVVL ...String:
MFKNAFANLQ KVGKSLMLPV SVLPIAGILL GVGSANFSWL PAVVSHVMAE AGGSVFANMP LIFAIGVALG FTNNDGVSAL AAVVAYGIM VKTMAVVAPL VLHLPAEEIA SKHLADTGVL GGIISGAIAA YMFNRFYRIK LPEYLGFFAG KRFVPIISGL A AIFTGVVL SFIWPPIGSA IQTFSQWAAY QNPVVAFGIY GFIERCLVPF GLHHIWNVPF QMQIGEYTNA AGQVFHGDIP RY MAGDPTA GKLSGGFLFK MYGLPAAAIA IWHSAKPENR AKVGGIMISA ALTSFLTGIT EPIEFSFMFV APILYIIHAI LAG LAFPIC ILLGMRDGTS FSHGLIDFIV LSGNSSKLWL FPIVGIGYAI VYYTIFRVLI KALDLKTPGR EDATEDAKAT GTSE MAPAL VAAFGGKENI TNLDACITRL RVSVADVSKV DQAGLKKLGA AGVVVAGSGV QAIFGTKSDN LKTEMDEYIR NH

UniProtKB: PTS system glucose-specific EIICB component

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Macromolecule #2: DNA-binding transcriptional repressor Mlc

MacromoleculeName: DNA-binding transcriptional repressor Mlc / type: protein_or_peptide / ID: 2 / 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 #3: beta-D-glucopyranose

MacromoleculeName: beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 4 / Formula: BGC
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-BGC:
beta-D-glucopyranose

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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

Concentration5.0 mg/mL
BufferpH: 8
Details: 20 mM HEPES-NaOH pH 8.0, 100 mM NaCl, 5 mM b-ME, 0.02% (w/v) DDM, 5 mM D-glucose
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 19806 / Average exposure time: 1.49 sec. / Average electron dose: 50.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 105000
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: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 406110
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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