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- EMDB-45181: The structure of two MntR dimers bound to the native mnep promote... -

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Basic information

Entry
Database: EMDB / ID: EMD-45181
TitleThe structure of two MntR dimers bound to the native mnep promoter sequence.
Map dataSharpened cryo-EM map of 2 MntR dimers bound to the native mnep sequence.
Sample
  • Complex: MntR bound to mnep promoter sequence
    • Complex: MntR
      • Protein or peptide: HTH-type transcriptional regulator MntR
    • Complex: mnep promoter sequence
      • DNA: DNA (39-MER)
      • DNA: DNA (38-MER)
  • Ligand: MANGANESE (II) ION
KeywordsManganese / metal ion homeostasis / transcription regulation / transcription activation / cooperative 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: 3.09 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 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45181.png

Downloads & links

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Map

FileDownload / File: emd_45181.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened cryo-EM map of 2 MntR dimers bound to the native mnep sequence.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 256 pix.
= 255.601 Å		1 Å/pix.
x 256 pix.
= 255.601 Å		1 Å/pix.
x 256 pix.
= 255.601 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.99844 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.2651898 - 1.9341338
Average (Standard dev.)0.00041640672 (±0.023269236)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 255.60065 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45181_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened cryo-EM map of 2 MntR dimers bound...

Fileemd_45181_additional_1.map
AnnotationUnsharpened cryo-EM map of 2 MntR dimers bound to the native mnep 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 reconstruction of 2 MntR...

Fileemd_45181_half_map_1.map
AnnotationHalf-map A used for reconstruction of 2 MntR dimers bound to the native mnep 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 reconstruction of 2 MntR...

Fileemd_45181_half_map_2.map
AnnotationHalf-map B used for reconstruction of 2 MntR dimers bound to the native mnep 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 : MntR bound to mnep promoter sequence

EntireName: MntR bound to mnep promoter sequence
Components
  • Complex: MntR bound to mnep promoter sequence
    • Complex: MntR
      • Protein or peptide: HTH-type transcriptional regulator MntR
    • Complex: mnep promoter sequence
      • DNA: DNA (39-MER)
      • DNA: DNA (38-MER)
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: MntR bound to mnep promoter sequence

SupramoleculeName: MntR bound to mnep promoter sequence / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: MntR

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

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Supramolecule #3: mnep promoter sequence

SupramoleculeName: mnep promoter sequence / 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 (39-MER)

MacromoleculeName: DNA (39-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 11.936714 KDa
SequenceString:
(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)

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Macromolecule #2: DNA (38-MER)

MacromoleculeName: DNA (38-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 11.748625 KDa
SequenceString:
(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)

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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: 4 / 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: 8 / 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) / Detector mode: SUPER-RESOLUTION / 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: PDB ENTRY
PDB model - PDB ID:

1on1

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 194072
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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