[English] 日本語
Yorodumi
- EMDB-55160: Cryo-EM structure of the Mlc tetramer in complex with the anti-re... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-55160
TitleCryo-EM structure of the Mlc tetramer in complex with the anti-repressor MtfA
Map dataComposite map
Sample
  • Complex: Mlc tetramer in complex with the anti-repressor MtfA
    • Protein or peptide: Mlc titration factor A
    • Protein or peptide: DNA-binding transcriptional repressor Mlc
  • Ligand: ZINC ION
KeywordsRepressor / DNA-binding protein / transcription regulation / gene regulation / carbohydrate utilization / metal-binding / anti-repressor / Metalloprotease / Hydrolase / DNA BINDING PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 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

-
Structure visualization

Supplemental images

emd_55160.png

Downloads & links

-
Map

FileReleased
AnnotationComposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 300 pix.
= 337.53 Å		1.13 Å/pix.
x 300 pix.
= 337.53 Å		1.13 Å/pix.
x 300 pix.
= 337.53 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1251 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.07018419 - 2.6158347
Average (Standard dev.)0.00093898625 (±0.021519905)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 337.53 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Mlc tetramer in complex with the anti-repressor MtfA

EntireName: Mlc tetramer in complex with the anti-repressor MtfA
Components
  • Complex: Mlc tetramer in complex with the anti-repressor MtfA
    • Protein or peptide: Mlc titration factor A
    • Protein or peptide: DNA-binding transcriptional repressor Mlc
  • Ligand: ZINC ION

-
Supramolecule #1: Mlc tetramer in complex with the anti-repressor MtfA

SupramoleculeName: Mlc tetramer in complex with the anti-repressor MtfA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: Mlc titration factor A

MacromoleculeName: Mlc titration factor A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 33.026996 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIKWPWKVQE SAHQTALPWQ EALSIPLLTC LTEQEQSKLV TLAERFLQQK RLVPLQGFEL DSLRSCRIAL LFCLPVLELG LEWLDGFHE VLIYPAPFVV DDEWEDDIGL VHNQRIVQSG QSWQQGPIVL NWLDIQDSFD ASGFNLIIHE VAHKLDTRNG D RASGVPFI ...String:
MIKWPWKVQE SAHQTALPWQ EALSIPLLTC LTEQEQSKLV TLAERFLQQK RLVPLQGFEL DSLRSCRIAL LFCLPVLELG LEWLDGFHE VLIYPAPFVV DDEWEDDIGL VHNQRIVQSG QSWQQGPIVL NWLDIQDSFD ASGFNLIIHE VAHKLDTRNG D RASGVPFI PLREVAGWEH DLHAAMNNIQ EEIELVGENA ASIDAYAASD PAECFAVLSE YFFSAPELFA PRFPSLWQRF CQ FYQQDPL QRLHHANDTD SFSATNVHLE LEVLFQGPVD HHHHHHHHHH

UniProtKB: Mlc titration factor A

-
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

-
Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.5 mg/mL
BufferpH: 8
Details: 20 mM HEPES-NaOH pH 8.0, 150 mM NaCl, 1 mM b-ME, 5 uM ZnCl2
VitrificationCryogen name: ETHANE

-
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: 7521 / Average exposure time: 3.57 sec. / Average electron dose: 30.0 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 / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
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: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1469021
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more