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Yorodumi- PDB-7ckq: The cryo-EM structure of B. subtilis BmrR transcription activatio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ckq | ||||||
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Title | The cryo-EM structure of B. subtilis BmrR transcription activation complex | ||||||
Components |
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Keywords | TRANSCRIPTION / RNA polymerase / Transcription activation | ||||||
Function / homology | Function and homology information nucleoid / sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-binding transcription factor activity / response to antibiotic ...nucleoid / sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-binding transcription factor activity / response to antibiotic / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å | ||||||
Authors | Fang, C.L. / Zhang, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2020 Title: The bacterial multidrug resistance regulator BmrR distorts promoter DNA to activate transcription. Authors: Chengli Fang / Linyu Li / Yihan Zhao / Xiaoxian Wu / Steven J Philips / Linlin You / Mingkang Zhong / Xiaojin Shi / Thomas V O'Halloran / Qunyi Li / Yu Zhang / Abstract: The MerR-family proteins represent a unique family of bacteria transcription factors (TFs), which activate transcription in a manner distinct from canonical ones. Here, we report a cryo-EM structure ...The MerR-family proteins represent a unique family of bacteria transcription factors (TFs), which activate transcription in a manner distinct from canonical ones. Here, we report a cryo-EM structure of a B. subtilis transcription activation complex comprising B. subtilis six-subunit (2αββ'ωε) RNA Polymerase (RNAP) core enzyme, σ, a promoter DNA, and the ligand-bound B. subtilis BmrR, a prototype of MerR-family TFs. The structure reveals that RNAP and BmrR recognize the upstream promoter DNA from opposite faces and induce four significant kinks from the -35 element to the -10 element of the promoter DNA in a cooperative manner, which restores otherwise inactive promoter activity by shortening the length of promoter non-optimal -35/-10 spacer. Our structure supports a DNA-distortion and RNAP-non-contact paradigm of transcriptional activation by MerR TFs. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ckq.cif.gz | 654 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ckq.ent.gz | 504.2 KB | Display | PDB format |
PDBx/mmJSON format | 7ckq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/7ckq ftp://data.pdbj.org/pub/pdb/validation_reports/ck/7ckq | HTTPS FTP |
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-Related structure data
Related structure data | 30390MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE
#1: Protein | Mass: 34842.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / Strain: 168 / References: UniProt: P20429, DNA-directed RNA polymerase #2: Protein | | Mass: 133847.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / Strain: 168 / References: UniProt: P37870, DNA-directed RNA polymerase #3: Protein | | Mass: 134444.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / Strain: 168 / References: UniProt: P37871, DNA-directed RNA polymerase #4: Protein | | Mass: 7766.921 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / Strain: 168 / References: UniProt: O35011, DNA-directed RNA polymerase |
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-Protein , 3 types, 4 molecules FGIH
#5: Protein | Mass: 43007.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / Strain: 168 / References: UniProt: P06224 | ||
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#8: Protein | Mass: 32951.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: bmrR, bmr1R, BSU24020 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39075 #9: Protein | | Mass: 8263.358 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (strain 168) (bacteria) / Strain: 168 / References: UniProt: O31718 |
-DNA chain , 2 types, 2 molecules 12
#6: DNA chain | Mass: 15489.907 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#7: DNA chain | Mass: 15485.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 5 molecules
#10: Chemical | ChemComp-MG / | ||
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#11: Chemical | #12: Chemical | |
-Details
Has ligand of interest | N |
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-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 | Name: Bacillus subtilis BmrR transcription activation complex Type: COMPLEX / Entity ID: #1-#9 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.48 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 19 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 282.65 K |
-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 FIELDBright-field microscopy / Cs: 2.7 mm |
Image recording | Average exposure time: 7.6 sec. / Electron dose: 60.8 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2226 |
Image scans | Movie frames/image: 38 |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 494295 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103226 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||||||||||
Atomic model building |
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