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- EMDB-45182: The structure of 4 MntR homodimers bound to the promoter sequence... -

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Basic information

Entry
Database: EMDB / ID: EMD-45182
TitleThe structure of 4 MntR homodimers bound to the promoter sequence of mnep.
Map dataSharpened map from cryo-EM reconstruction of 4 MntR homodimers bound to the mnep promoter sequence.
Sample
  • Complex: The complex of 4 MntR homodimers bound to DNA.
    • Complex: MntR homodimers
      • Protein or peptide: HTH-type transcriptional regulator MntR
    • Complex: DNA
      • DNA: DNA (77-MER)
      • DNA: DNA (77-MER)
  • Ligand: MANGANESE (II) ION
KeywordsManganese / metal ion homeostasis / cooperative binding / DNA binding / GENE REGULATION
Function / homology
Function and homology information


intracellular manganese ion homeostasis / manganese ion binding / protein dimerization activity / DNA-binding transcription factor activity / DNA binding / cytoplasm
Similarity search - Function
HTH-type transcription regulator MntR / : / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain / Iron dependent repressor / Iron dependent repressor, metal binding and dimerisation domain superfamily / Iron dependent repressor, metal binding and dimerisation domain / Helix-turn-helix diphteria tox regulatory element ...HTH-type transcription regulator MntR / : / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain / Iron dependent repressor / Iron dependent repressor, metal binding and dimerisation domain superfamily / Iron dependent repressor, metal binding and dimerisation domain / Helix-turn-helix diphteria tox regulatory element / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
HTH-type transcriptional regulator MntR
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.17 Å
AuthorsShi H / Fu Y / Glasfeld A / Ahuja S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for transcription activation through cooperative recruitment of MntR.
Authors: Haoyuan Shi / Yu Fu / Vilmante Kodyte / Amelie Andreas / Ankita J Sachla / Keikilani Miller / Ritu Shrestha / John D Helmann / Arthur Glasfeld / Shivani Ahuja /
Abstract: Bacillus subtilis MntR is a dual regulatory protein that responds to heightened Mn availability in the cell by both repressing the expression of uptake transporters and activating the expression of ...Bacillus subtilis MntR is a dual regulatory protein that responds to heightened Mn availability in the cell by both repressing the expression of uptake transporters and activating the expression of efflux proteins. Recent work indicates that, in its role as an activator, MntR binds several sites upstream of the genes encoding Mn exporters, leading to a cooperative response to manganese. Here, we use cryo-EM to explore the molecular basis of gene activation by MntR and report a structure of four MntR dimers bound to four 18-base pair sites across an 84-base pair regulatory region of the mneP promoter. Our structures, along with solution studies including mass photometry and in vivo transcription assays, reveal that MntR dimers employ polar and non-polar contacts to bind cooperatively to an array of low-affinity DNA-binding sites. These results reveal the molecular basis for cooperativity in the activation of manganese efflux.
History
DepositionJun 4, 2024-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45182.png

Downloads & links

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Map

FileDownload / File: emd_45182.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map from cryo-EM reconstruction of 4 MntR homodimers bound to the mnep promoter sequence.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 512 pix.
= 852.019 Å		1.66 Å/pix.
x 512 pix.
= 852.019 Å		1.66 Å/pix.
x 512 pix.
= 852.019 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.6641 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.29
Minimum - Maximum-0.5978374 - 1.3105855
Average (Standard dev.)-0.000095823336 (±0.011998304)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 852.0192 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45182_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map from cryo-EM reconstruction of 4 MntR...

Fileemd_45182_additional_1.map
AnnotationUnsharpened map from cryo-EM reconstruction of 4 MntR homodimers bound to the mnep promoter sequence.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A used for cryo-EM reconstruction of...

Fileemd_45182_half_map_1.map
AnnotationHalf map A used for cryo-EM reconstruction of 4 MntR homodimers bound to the mnep promoter sequence.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B used for cryo-EM reconstruction of...

Fileemd_45182_half_map_2.map
AnnotationHalf map B used for cryo-EM reconstruction of 4 MntR homodimers bound to the mnep promoter sequence.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The complex of 4 MntR homodimers bound to DNA.

EntireName: The complex of 4 MntR homodimers bound to DNA.
Components
  • Complex: The complex of 4 MntR homodimers bound to DNA.
    • Complex: MntR homodimers
      • Protein or peptide: HTH-type transcriptional regulator MntR
    • Complex: DNA
      • DNA: DNA (77-MER)
      • DNA: DNA (77-MER)
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: The complex of 4 MntR homodimers bound to DNA.

SupramoleculeName: The complex of 4 MntR homodimers bound to DNA. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: MntR homodimers

SupramoleculeName: MntR homodimers / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Bacillus subtilis (bacteria)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Bacillus subtilis (bacteria) / Synthetically produced: Yes

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Macromolecule #1: DNA (77-MER)

MacromoleculeName: DNA (77-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 23.546127 KDa
SequenceString: (DT)(DT)(DT)(DT)(DT)(DA)(DG)(DC)(DA)(DT) (DA)(DG)(DC)(DT)(DC)(DC)(DA)(DA)(DC)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DC)(DT)(DG) (DT)(DC)(DA)(DC)(DC)(DT)(DT)(DA)(DT)(DT) (DT) (DA)(DT)(DT)(DA)(DG)(DT) ...String:
(DT)(DT)(DT)(DT)(DT)(DA)(DG)(DC)(DA)(DT) (DA)(DG)(DC)(DT)(DC)(DC)(DA)(DA)(DC)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DC)(DT)(DG) (DT)(DC)(DA)(DC)(DC)(DT)(DT)(DA)(DT)(DT) (DT) (DA)(DT)(DT)(DA)(DG)(DT)(DA)(DA) (DA)(DC)(DA)(DG)(DG)(DA)(DA)(DA)(DC)(DA) (DA)(DC) (DG)(DT)(DT)(DG)(DC)(DT)(DA) (DT)(DA)(DG)(DA)(DC)(DC)(DC)(DA)(DC)(DT)

GENBANK: GENBANK: CP058242.1

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Macromolecule #2: DNA (77-MER)

MacromoleculeName: DNA (77-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 23.929418 KDa
SequenceString: (DA)(DG)(DT)(DG)(DG)(DG)(DT)(DC)(DT)(DA) (DT)(DA)(DG)(DC)(DA)(DA)(DC)(DG)(DT)(DT) (DG)(DT)(DT)(DT)(DC)(DC)(DT)(DG)(DT) (DT)(DT)(DA)(DC)(DT)(DA)(DA)(DT)(DA)(DA) (DA) (DT)(DA)(DA)(DG)(DG)(DT) ...String:
(DA)(DG)(DT)(DG)(DG)(DG)(DT)(DC)(DT)(DA) (DT)(DA)(DG)(DC)(DA)(DA)(DC)(DG)(DT)(DT) (DG)(DT)(DT)(DT)(DC)(DC)(DT)(DG)(DT) (DT)(DT)(DA)(DC)(DT)(DA)(DA)(DT)(DA)(DA) (DA) (DT)(DA)(DA)(DG)(DG)(DT)(DG)(DA) (DC)(DA)(DG)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DG)(DT) (DT)(DG)(DG)(DA)(DG)(DC)(DT) (DA)(DT)(DG)(DC)(DT)(DA)(DA)(DA)(DA)(DA)

GENBANK: GENBANK: CP058242.1

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Macromolecule #3: HTH-type transcriptional regulator MntR

MacromoleculeName: HTH-type transcriptional regulator MntR / type: protein_or_peptide / ID: 3 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 16.787133 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTTPSMEDYI EQIYMLIEEK GYARVSDIAE ALAVHPSSVT KMVQKLDKDE YLIYEKYRGL VLTSKGKKIG KRLVYRHELL EQFLRIIGV DEEKIYNDVE GIEHHLSWNS IDRIGDLVQY FEEDDARKKD LKSIQKKTEH HNQ

UniProtKB: HTH-type transcriptional regulator MntR

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Macromolecule #4: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 4 / Number of copies: 16 / Formula: MN
Molecular weightTheoretical: 54.938 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

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 228659
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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