+Open data
-Basic information
Entry | Database: PDB / ID: 7ubj | ||||||
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Title | Transcription antitermination factor Qlambda, type-I crystal | ||||||
Components | Antitermination protein Q | ||||||
Keywords | GENE REGULATION / RNA polymerase / DNA Binding / transcription / Q-dependent antitermination / Q antitermination factor | ||||||
Function / homology | Function and homology information transcription antitermination / DNA-templated transcription termination / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Escherichia phage Lambda (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.46 Å | ||||||
Authors | Yin, Z. / Ebright, R.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2022 Title: In transcription antitermination by Qλ, NusA induces refolding of Qλ to form a nozzle that extends the RNA polymerase RNA-exit channel. Authors: Zhou Yin / Jeremy G Bird / Jason T Kaelber / Bryce E Nickels / Richard H Ebright / Abstract: Lambdoid bacteriophage Q proteins are transcription antipausing and antitermination factors that enable RNA polymerase (RNAP) to read through pause and termination sites. Q proteins load onto RNAP ...Lambdoid bacteriophage Q proteins are transcription antipausing and antitermination factors that enable RNA polymerase (RNAP) to read through pause and termination sites. Q proteins load onto RNAP engaged in promoter-proximal pausing at a Q binding element (QBE) and adjacent sigma-dependent pause element to yield a Q-loading complex, and they translocate with RNAP as a pausing-deficient, termination-deficient Q-loaded complex. In previous work, we showed that the Q protein of bacteriophage 21 (Q21) functions by forming a nozzle that narrows and extends the RNAP RNA-exit channel, preventing formation of pause and termination RNA hairpins. Here, we report atomic structures of four states on the pathway of antitermination by the Q protein of bacteriophage λ (Qλ), a Q protein that shows no sequence similarity to Q21 and that, unlike Q21, requires the transcription elongation factor NusA for efficient antipausing and antitermination. We report structures of Qλ, the Qλ-QBE complex, the NusA-free pre-engaged Qλ-loading complex, and the NusA-containing engaged Qλ-loading complex. The results show that Qλ, like Q21, forms a nozzle that narrows and extends the RNAP RNA-exit channel, preventing formation of RNA hairpins. However, the results show that Qλ has no three-dimensional structural similarity to Q21, employs a different mechanism of QBE recognition than Q21, and employs a more complex process for loading onto RNAP than Q21, involving recruitment of Qλ to form a pre-engaged loading complex, followed by NusA-facilitated refolding of Qλ to form an engaged loading complex. The results establish that Qλ and Q21 are not structural homologs and are solely functional analogs. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ubj.cif.gz | 137.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ubj.ent.gz | 106.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ubj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ubj_validation.pdf.gz | 472.9 KB | Display | wwPDB validaton report |
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Full document | 7ubj_full_validation.pdf.gz | 474.4 KB | Display | |
Data in XML | 7ubj_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 7ubj_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/7ubj ftp://data.pdbj.org/pub/pdb/validation_reports/ub/7ubj | HTTPS FTP |
-Related structure data
Related structure data | 7ubkC 7ublC 7ubmC 7ubnC 4mo1S S: Starting model for refinement 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 16222.834 Da / Num. of mol.: 2 / Fragment: UNP residues 62-207 / Mutation: E134K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia phage Lambda (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: P03047 |
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-Non-polymers , 7 types, 461 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | #7: Chemical | ChemComp-PO4 / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.47 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% v/v glycerol, 0.4 M potassium phosphate dibasic, 16% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.987 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 5, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.46→50 Å / Num. obs: 63011 / % possible obs: 99.7 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.024 / Rrim(I) all: 0.055 / Χ2: 0.85 / Net I/σ(I): 11.9 / Num. measured all: 319426 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4MO1 Resolution: 1.46→43.273 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 22.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.93 Å2 / Biso mean: 23.5208 Å2 / Biso min: 4.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.46→43.273 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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