+Open data
-Basic information
Entry | Database: PDB / ID: 6wmr | ||||||
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Title | F. tularensis RNAPs70-(MglA-SspA)-iglA DNA complex | ||||||
Components |
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Keywords | TRANSCRIPTION / RNA polymerase complex | ||||||
Function / homology | Function and homology information sigma factor activity / glutathione metabolic process / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / transferase activity / protein dimerization activity / DNA-templated transcription ...sigma factor activity / glutathione metabolic process / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / transferase activity / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Francisella tularensis subsp. holarctica LVS (bacteria) Francisella tularensis subsp. holarctica (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.46 Å | ||||||
Authors | Travis, B.A. / Brennan, R.G. / Schumacher, M.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Mol Cell / Year: 2021 Title: Structural Basis for Virulence Activation of Francisella tularensis. Authors: Brady A Travis / Kathryn M Ramsey / Samantha M Prezioso / Thomas Tallo / Jamie M Wandzilak / Allen Hsu / Mario Borgnia / Alberto Bartesaghi / Simon L Dove / Richard G Brennan / Maria A Schumacher / Abstract: The bacterium Francisella tularensis (Ft) is one of the most infectious agents known. Ft virulence is controlled by a unique combination of transcription regulators: the MglA-SspA heterodimer, PigR, ...The bacterium Francisella tularensis (Ft) is one of the most infectious agents known. Ft virulence is controlled by a unique combination of transcription regulators: the MglA-SspA heterodimer, PigR, and the stress signal, ppGpp. MglA-SspA assembles with the σ-associated RNAP holoenzyme (RNAPσ), forming a virulence-specialized polymerase. These factors activate Francisella pathogenicity island (FPI) gene expression, which is required for virulence, but the mechanism is unknown. Here we report FtRNAPσ-promoter-DNA, FtRNAPσ-(MglA-SspA)-promoter DNA, and FtRNAPσ-(MglA-SspA)-ppGpp-PigR-promoter DNA cryo-EM structures. Structural and genetic analyses show MglA-SspA facilitates σ binding to DNA to regulate virulence and virulence-enhancing genes. Our Escherichia coli RNAPσhomodimeric EcSspA structure suggests this is a general SspA-transcription regulation mechanism. Strikingly, our FtRNAPσ-(MglA-SspA)-ppGpp-PigR-DNA structure reveals ppGpp binding to MglA-SspA tethers PigR to promoters. PigR in turn recruits FtRNAP αCTDs to DNA UP elements. Thus, these studies unveil a unique mechanism for Ft pathogenesis involving a virulence-specialized RNAP that employs two (MglA-SspA)-based strategies to activate virulence genes. | ||||||
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 | 6wmr.cif.gz | 723.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wmr.ent.gz | 552.9 KB | Display | PDB format |
PDBx/mmJSON format | 6wmr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/6wmr ftp://data.pdbj.org/pub/pdb/validation_reports/wm/6wmr | HTTPS FTP |
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-Related structure data
Related structure data | 21851MC 6wegC 6wmpC 6wmtC 6wmuC 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 chain , 4 types, 4 molecules GHXJ
#1: DNA chain | Mass: 10819.960 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Francisella tularensis subsp. holarctica LVS (bacteria) |
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#2: DNA chain | Mass: 7283.774 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Francisella tularensis subsp. holarctica LVS (bacteria) |
#3: DNA chain | Mass: 3350.185 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Francisella tularensis subsp. holarctica LVS (bacteria) |
#4: DNA chain | Mass: 3359.199 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Francisella tularensis subsp. holarctica LVS (bacteria) |
-Protein , 3 types, 3 molecules SMZ
#5: Protein | Mass: 24098.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Francisella tularensis subsp. holarctica LVS (bacteria) References: UniProt: A0A3N3ZVL6 |
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#6: Protein | Mass: 23650.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Francisella tularensis subsp. holarctica LVS (bacteria) References: UniProt: A0A0B6CT24 |
#7: Protein | Mass: 67748.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Francisella tularensis subsp. holarctica LVS (bacteria) References: UniProt: A0A0B3WH85 |
-DNA-directed RNA polymerase subunit ... , 5 types, 5 molecules ABCDE
#8: Protein | Mass: 35393.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Francisella tularensis subsp. holarctica (strain LVS) (bacteria) Strain: LVS / References: UniProt: Q2A5E5, DNA-directed RNA polymerase |
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#9: Protein | Mass: 35113.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Francisella tularensis subsp. holarctica (strain LVS) (bacteria) Strain: LVS / References: UniProt: Q2A4H7, DNA-directed RNA polymerase |
#10: Protein | Mass: 151536.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Francisella tularensis subsp. holarctica (strain LVS) (bacteria) Strain: LVS / References: UniProt: Q2A1M7, DNA-directed RNA polymerase |
#11: Protein | Mass: 157599.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Francisella tularensis subsp. holarctica (strain LVS) (bacteria) Strain: LVS / References: UniProt: Q2A1M8, DNA-directed RNA polymerase |
#12: Protein | Mass: 8184.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Francisella tularensis subsp. holarctica (strain LVS) (bacteria) Strain: LVS / References: UniProt: Q2A273, DNA-directed RNA polymerase |
-Non-polymers , 2 types, 3 molecules
#13: Chemical | ChemComp-MG / |
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#14: 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: Francisella RNAPs70-(MglA-SspA)-iglA complex / Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Francisella tularensis subsp. holarctica LVS (bacteria) |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.4 mg/ml / 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: OTHER |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Image recording | Electron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21457 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 128.39 Å2 | ||||||||||||||||||||||||
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