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Yorodumi- EMDB-45181: The structure of two MntR dimers bound to the native mnep promote... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-45181 | |||||||||
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Title | The structure of two MntR dimers bound to the native mnep promoter sequence. | |||||||||
Map data | Sharpened cryo-EM map of 2 MntR dimers bound to the native mnep sequence. | |||||||||
Sample |
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Keywords | Manganese / 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 | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.09 Å | |||||||||
Authors | Shi H / Fu Y / Glasfeld A / Ahuja S | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: The structure of two MntR dimers bound to the native mnep promoter sequence. Authors: Shi H / Fu Y / Glasfeld A / Ahuja S | |||||||||
History |
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-Structure visualization
-Downloads & links
-EMDB archive
Map data | EMDB map data format | |||
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Header (meta data) | EMDB header | |||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-45181 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-45181 | HTTPS FTP |
-Related structure data
Related structure data | 9c4cMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_45181.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Sharpened cryo-EM map of 2 MntR dimers bound to the native mnep sequence. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.99844 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : MntR bound to mnep promoter sequence
Entire | Name: MntR bound to mnep promoter sequence |
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Components |
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-Supramolecule #1: MntR bound to mnep promoter sequence
Supramolecule | Name: MntR bound to mnep promoter sequence / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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-Supramolecule #2: MntR
Supramolecule | Name: MntR / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: Bacillus subtilis (bacteria) |
-Supramolecule #3: mnep promoter sequence
Supramolecule | Name: mnep promoter sequence / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Bacillus subtilis (bacteria) / Synthetically produced: Yes |
-Macromolecule #1: DNA (39-MER)
Macromolecule | Name: DNA (39-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Bacillus subtilis (bacteria) |
Molecular weight | Theoretical: 11.936714 KDa |
Sequence | String: (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) |
-Macromolecule #2: DNA (38-MER)
Macromolecule | Name: DNA (38-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Bacillus subtilis (bacteria) |
Molecular weight | Theoretical: 11.748625 KDa |
Sequence | String: (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) |
-Macromolecule #3: HTH-type transcriptional regulator MntR
Macromolecule | Name: HTH-type transcriptional regulator MntR / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus subtilis (bacteria) |
Molecular weight | Theoretical: 16.787133 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTTPSMEDYI EQIYMLIEEK GYARVSDIAE ALAVHPSSVT KMVQKLDKDE YLIYEKYRGL VLTSKGKKIG KRLVYRHELL EQFLRIIGV DEEKIYNDVE GIEHHLSWNS IDRIGDLVQY FEEDDARKKD LKSIQKKTEH HNQ UniProtKB: HTH-type transcriptional regulator MntR |
-Macromolecule #4: MANGANESE (II) ION
Macromolecule | Name: MANGANESE (II) ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: MN |
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Molecular weight | Theoretical: 54.938 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 194072 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |