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Yorodumi- PDB-9c4c: The structure of two MntR dimers bound to the native mnep promote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9c4c | ||||||
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Title | The structure of two MntR dimers bound to the native mnep promoter sequence | ||||||
Components |
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Keywords | GENE 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 | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.09 Å | ||||||
Authors | Shi, H. / Fu, Y. / Glasfeld, A. / Ahuja, S. | ||||||
Funding support | 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9c4c.cif.gz | 281.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9c4c.ent.gz | 226.9 KB | Display | PDB format |
PDBx/mmJSON format | 9c4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/9c4c ftp://data.pdbj.org/pub/pdb/validation_reports/c4/9c4c | HTTPS FTP |
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-Related structure data
Related structure data | 45181 M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: DNA chain | Mass: 11936.714 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria) | ||||
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#2: DNA chain | Mass: 11748.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria) | ||||
#3: Protein | 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 / Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||
Buffer solution | pH: 7 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 194072 / Symmetry type: POINT | ||||||||||||||||||||||||
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