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Yorodumi- PDB-7xl3: Cryo-EM structure of Pseudomonas aeruginosa RNAP sigmaS holoenzym... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xl3 | |||||||||
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Title | Cryo-EM structure of Pseudomonas aeruginosa RNAP sigmaS holoenzyme complexes with transcription factor SutA (open lobe) | |||||||||
Components |
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Keywords | TRANSCRIPTION / transcription initiation / Pseudomonas aeruginosa / RNA polymerase / sigmaS / SutA / RNAP beta lobe / open beta lobe | |||||||||
Function / homology | Function and homology information regulation of response to salt stress / negative regulation of secondary metabolite biosynthetic process / positive regulation of single-species biofilm formation on inanimate substrate / regulation of cellular response to oxidative stress / positive regulation of chemotaxis / regulation of cell motility / sigma factor activity / DNA-directed RNA polymerase complex / regulation of cellular response to heat / DNA-templated transcription initiation ...regulation of response to salt stress / negative regulation of secondary metabolite biosynthetic process / positive regulation of single-species biofilm formation on inanimate substrate / regulation of cellular response to oxidative stress / positive regulation of chemotaxis / regulation of cell motility / sigma factor activity / DNA-directed RNA polymerase complex / regulation of cellular response to heat / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 Å | |||||||||
Authors | He, D.W. / You, L.L. / Zhang, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nat Commun / Year: 2022 Title: Pseudomonas aeruginosa SutA wedges RNAP lobe domain open to facilitate promoter DNA unwinding. Authors: Dingwei He / Linlin You / Xiaoxian Wu / Jing Shi / Aijia Wen / Zhi Yan / Wenhui Mu / Chengli Fang / Yu Feng / Yu Zhang / Abstract: Pseudomonas aeruginosa (Pae) SutA adapts bacteria to hypoxia and nutrition-limited environment during chronic infection by increasing transcription activity of an RNA polymerase (RNAP) holoenzyme ...Pseudomonas aeruginosa (Pae) SutA adapts bacteria to hypoxia and nutrition-limited environment during chronic infection by increasing transcription activity of an RNA polymerase (RNAP) holoenzyme comprising the stress-responsive σ factor σ (RNAP-σ). SutA shows no homology to previously characterized RNAP-binding proteins. The structure and mode of action of SutA remain unclear. Here we determined cryo-EM structures of Pae RNAP-σ holoenzyme, Pae RNAP-σ holoenzyme complexed with SutA, and Pae RNAP-σ transcription initiation complex comprising SutA. The structures show SutA pinches RNAP-β protrusion and facilitates promoter unwinding by wedging RNAP-β lobe open. Our results demonstrate that SutA clears an energetic barrier to facilitate promoter unwinding of RNAP-σ holoenzyme. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xl3.cif.gz | 601.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xl3.ent.gz | 470.9 KB | Display | PDB format |
PDBx/mmJSON format | 7xl3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xl3_validation.pdf.gz | 832.5 KB | Display | wwPDB validaton report |
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Full document | 7xl3_full_validation.pdf.gz | 853.4 KB | Display | |
Data in XML | 7xl3_validation.xml.gz | 88.6 KB | Display | |
Data in CIF | 7xl3_validation.cif.gz | 136.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/7xl3 ftp://data.pdbj.org/pub/pdb/validation_reports/xl/7xl3 | HTTPS FTP |
-Related structure data
Related structure data | 33271MC 7f0rC 7vf9C 7xl4C 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
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE
#1: Protein | Mass: 38264.258 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: rpoA, PA4238 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O52760, DNA-directed RNA polymerase #2: Protein | | Mass: 151225.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: rpoB, PA4270 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q51561, DNA-directed RNA polymerase #3: Protein | | Mass: 156038.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: rpoC, PA4269 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HWC9, DNA-directed RNA polymerase #4: Protein | | Mass: 9783.876 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: rpoZ, PA5337 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HTM1, DNA-directed RNA polymerase |
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-Protein , 2 types, 2 molecules GF
#5: Protein | Mass: 11497.365 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: PA5285 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HTR9 |
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#6: Protein | Mass: 38606.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: rpoS, PA3622 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P45684 |
-Non-polymers , 2 types, 3 molecules
#7: Chemical | #8: Chemical | ChemComp-MG / | |
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-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: Pseudomonas aeruginosa RNAP sigmaS holoenzyme with transcription factor SutA complex(open lobe) Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT |
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Molecular weight | Value: 0.433 MDa / Experimental value: YES |
Source (natural) | Organism: Pseudomonas aeruginosa PAO1 (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283 K / Details: blot 4s before plunging |
-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 magnification: 64000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm / Cs: 0 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 138109 / Symmetry type: POINT |