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- PDB-9srw: Cryo-EM structure of the Mlc tetramer in complex with the anti-re... -

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Basic information

Entry
Database: PDB / ID: 9srw
TitleCryo-EM structure of the Mlc tetramer in complex with the anti-repressor MtfA
Components
  • DNA-binding transcriptional repressor Mlc
  • Mlc titration factor A
KeywordsDNA BINDING PROTEIN / Repressor / DNA-binding protein / transcription regulation / gene regulation / carbohydrate utilization / metal-binding / anti-repressor / Metalloprotease / Hydrolase
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / aminopeptidase activity / metallopeptidase activity / regulation of DNA-templated transcription / DNA-templated transcription / proteolysis / DNA binding / zinc ion binding / membrane / metal ion binding ...Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / aminopeptidase activity / metallopeptidase activity / regulation of DNA-templated transcription / DNA-templated transcription / proteolysis / DNA binding / zinc ion binding / membrane / metal ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
MtfA family / MtfA, N-terminal / : / Glucose-regulated metallo-peptidase M90 / ROK family / ROK family / Metallopeptidase, catalytic domain superfamily / 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 / Mlc titration factor A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 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

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Assembly

Deposited unit
E: Mlc titration factor A
A: DNA-binding transcriptional repressor Mlc
B: DNA-binding transcriptional repressor Mlc
F: Mlc titration factor A
C: DNA-binding transcriptional repressor Mlc
D: DNA-binding transcriptional repressor Mlc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,05812
Polymers265,6666
Non-polymers3926
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 Mlc titration factor A / Mlc-binding protein / Probable zinc metallopeptidase MtfA


Mass: 33026.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mtfA, yeeI, b1976, JW1958 / Production host: Escherichia coli (E. coli)
References: UniProt: P76346, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases
#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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / 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 anti-repressor MtfA / 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, 150 mM NaCl, 1 mM b-ME, 5 uM ZnCl2
SpecimenConc.: 1.5 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: 130000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.57 sec. / Electron dose: 30 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7521
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1469021 / Symmetry type: POINT

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