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- PDB-9c4d: The structure of 4 MntR homodimers bound to the promoter sequence... -

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Basic information

Entry
Database: PDB / ID: 9c4d
TitleThe structure of 4 MntR homodimers bound to the promoter sequence of mnep
Components
  • (DNA (77-MER)) x 2
  • HTH-type transcriptional regulator MntR
KeywordsGENE REGULATION / Manganese / metal ion homeostasis / cooperative binding / DNA 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: 4.17 Å
AuthorsShi, H. / Fu, Y. / Glasfeld, A. / Ahuja, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The structure of 4 MntR homodimers bound to the promoter sequence of mnep.
Authors: Shi, H. / Fu, Y. / Glasfeld, A. / Ahuja, S.
History
DepositionJun 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (77-MER)
B: DNA (77-MER)
C: HTH-type transcriptional regulator MntR
D: HTH-type transcriptional regulator MntR
E: HTH-type transcriptional regulator MntR
F: HTH-type transcriptional regulator MntR
G: HTH-type transcriptional regulator MntR
H: HTH-type transcriptional regulator MntR
I: HTH-type transcriptional regulator MntR
J: HTH-type transcriptional regulator MntR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,65226
Polymers181,77310
Non-polymers87916
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 (77-MER)


Mass: 23546.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria) / References: GenBank: 1864548803
#2: DNA chain DNA (77-MER)


Mass: 23929.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria) / References: GenBank: 1864548803
#3: Protein
HTH-type transcriptional regulator MntR / Manganese transport regulator / Manganese(II) metalloregulatory protein MntR


Mass: 16787.133 Da / Num. of mol.: 8
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.: 16 / Source method: obtained synthetically / Formula: Mn
Has ligand of interestN

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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
1The complex of 4 MntR homodimers bound to DNA.COMPLEX#1-#30MULTIPLE SOURCES
2MntR homodimersCOMPLEX#31RECOMBINANT
3DNACOMPLEX#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 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 228659 / Symmetry type: POINT

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