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- PDB-9c4c: The structure of two MntR dimers bound to the native mnep promote... -

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Basic information

Entry
Database: PDB / ID: 9c4c
TitleThe structure of two MntR dimers bound to the native mnep promoter sequence
Components
  • DNA (38-MER)
  • DNA (39-MER)
  • HTH-type transcriptional regulator MntR
KeywordsGENE REGULATION / Manganese / metal ion homeostasis / transcription regulation / transcription activation / cooperative binding
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
: / DNA / DNA (> 10) / HTH-type transcriptional regulator MntR
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsShi, H. / Fu, Y. / Glasfeld, A. / Ahuja, S.
Funding support1items
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, 2024Deposition site: RCSB / Processing site: RCSB
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Revision 1.1Mar 12, 2025Group: Data collection / Database references / Structure summary
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (39-MER)
B: DNA (38-MER)
E: HTH-type transcriptional regulator MntR
F: HTH-type transcriptional regulator MntR
G: HTH-type transcriptional regulator MntR
H: HTH-type transcriptional regulator MntR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,27314
Polymers90,8346
Non-polymers4408
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: DNA chain DNA (39-MER)


Mass: 11936.714 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria)
#2: DNA chain DNA (38-MER)


Mass: 11748.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria)
#3: Protein
HTH-type transcriptional regulator MntR / Manganese transport regulator / Manganese(II) metalloregulatory protein MntR


Mass: 16787.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: mntR, yqhN, BSU24520 / Production host: Escherichia coli (E. coli) / References: UniProt: P54512
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
Has ligand of interestN
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

Component
IDNameTypeEntity IDParent-IDSource
1MntR bound to mnep promoter sequenceCOMPLEX#1-#30MULTIPLE SOURCES
2MntRCOMPLEX#31RECOMBINANT
3mnep promoter sequenceCOMPLEX#1-#21SYNTHETIC
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Bacillus subtilis (bacteria)1423
33Bacillus subtilis (bacteria)1423
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 194072 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0046330
ELECTRON MICROSCOPYf_angle_d0.6998844
ELECTRON MICROSCOPYf_dihedral_angle_d25.9731366
ELECTRON MICROSCOPYf_chiral_restr0.043978
ELECTRON MICROSCOPYf_plane_restr0.004849

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