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- PDB-9srx: Cryo-EM structure of the Mlc repressor in complex with the glucos... -

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Basic information

Entry
Database: PDB / ID: 9srx
TitleCryo-EM structure of the Mlc repressor in complex with the glucose-specific IICB transporter
Components
  • DNA-binding transcriptional repressor Mlc
  • PTS system glucose-specific EIICB component
KeywordsDNA BINDING PROTEIN / Repressor / DNA-binding protein / transcription regulation / gene regulation / carbohydrate utilization / metal-binding / membrane transporter / glucose / transmembrane protein / membrane-tethering
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
beta-D-glucopyranose / DNA-binding transcriptional repressor Mlc / PTS system glucose-specific EIICB component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsRoth, P. / Fotiadis, D.
Funding support Switzerland, 1items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
K: PTS system glucose-specific EIICB component
L: PTS system glucose-specific EIICB component
I: PTS system glucose-specific EIICB component
J: PTS system glucose-specific EIICB component
G: PTS system glucose-specific EIICB component
H: PTS system glucose-specific EIICB component
C: DNA-binding transcriptional repressor Mlc
D: DNA-binding transcriptional repressor Mlc
F: PTS system glucose-specific EIICB component
E: PTS system glucose-specific EIICB component
B: DNA-binding transcriptional repressor Mlc
A: DNA-binding transcriptional repressor Mlc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)606,34820
Polymers605,36612
Non-polymers9828
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
PTS system glucose-specific EIICB component / EIICB-Glc / EII-Glc


Mass: 50719.223 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ptsG, glcA, umg, b1101, JW1087 / Production host: Escherichia coli (E. coli)
References: UniProt: P69786, protein-Npi-phosphohistidine-D-glucose phosphotransferase
#2: Protein
DNA-binding transcriptional repressor Mlc / Making large colonies protein / Membrane linked control


Mass: 49902.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mlc, dgsA, b1594, JW1586 / Production host: Escherichia coli (E. coli) / References: UniProt: P50456
#3: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: Mlc tetramer in complex with the dimeric glucose-specific IICB transporter
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 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
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 700 nm
Image recordingAverage exposure time: 1.49 sec. / Electron dose: 50.3 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 19806
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
12cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 406110 / Symmetry type: POINT

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