+Open data
-Basic information
Entry | Database: PDB / ID: 7xyb | ||||||
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Title | The cryo-EM structure of an AlpA-loaded complex | ||||||
Components |
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Keywords | TRANSCRIPTION / Antitermination / RNA polymerase / Transcription regulation / Antiterminator / Transcription termination | ||||||
Function / homology | Function and homology information DNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Wen, A. / Feng, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Nucleic Acids Res / Year: 2022 Title: Structural basis of AlpA-dependent transcription antitermination. Authors: Aijia Wen / Minxing Zhao / Sha Jin / Yuan-Qiang Lu / Yu Feng / Abstract: AlpA positively regulates a programmed cell death pathway linked to the virulence of Pseudomonas aeruginosa by recognizing an AlpA binding element within the promoter, then binding RNA polymerase ...AlpA positively regulates a programmed cell death pathway linked to the virulence of Pseudomonas aeruginosa by recognizing an AlpA binding element within the promoter, then binding RNA polymerase directly and allowing it to bypass an intrinsic terminator positioned downstream. Here, we report the single-particle cryo-electron microscopy structures of both an AlpA-loading complex and an AlpA-loaded complex. These structures indicate that the C-terminal helix-turn-helix motif of AlpA binds to the AlpA binding element and that the N-terminal segment of AlpA forms a narrow ring inside the RNA exit channel. AlpA was also revealed to render RNAP resistant to termination signals by prohibiting RNA hairpin formation in the RNA exit channel. Structural analysis predicted that AlpA, 21Q, λQ and 82Q share the same mechanism of transcription antitermination. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xyb.cif.gz | 551.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xyb.ent.gz | 420.1 KB | Display | PDB format |
PDBx/mmJSON format | 7xyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/7xyb ftp://data.pdbj.org/pub/pdb/validation_reports/xy/7xyb | HTTPS FTP |
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-Related structure data
Related structure data | 33516MC 7xyaC 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: 36694.555 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: rpoA, PA4238 / Production host: Escherichia coli (E. coli) / References: UniProt: O52760, DNA-directed RNA polymerase #2: Protein | | Mass: 151037.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: rpoB, PA4270 / Production host: Escherichia coli (E. coli) / References: UniProt: Q51561, DNA-directed RNA polymerase #3: Protein | | Mass: 154595.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: rpoC, PA4269 / Production host: Escherichia coli (E. coli) / 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 (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: rpoZ, PA5337 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HTM1, DNA-directed RNA polymerase |
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-DNA chain , 2 types, 2 molecules NT
#7: DNA chain | Mass: 24919.896 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria) |
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#8: DNA chain | Mass: 23800.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria) |
-Protein / RNA chain / Non-polymers , 3 types, 3 molecules GR
#5: Protein | Mass: 20315.600 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: CSB93_5829 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2R3ITY7 |
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#6: RNA chain | Mass: 4622.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria) |
#9: Chemical | ChemComp-MG / |
-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: AlpA-loaded complex / Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
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 FIELDBright-field microscopy / Nominal defocus max: 1800 nm / Nominal defocus min: 900 nm |
Image recording | Electron dose: 52 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31470 / Symmetry type: POINT |