+Open data
-Basic information
Entry | Database: PDB / ID: 7ubk | ||||||
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Title | Transcription antitermination factor Qlambda, type-II 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: 1.97 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 | 7ubk.cif.gz | 183.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ubk.ent.gz | 146.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ubk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ubk_validation.pdf.gz | 455.1 KB | Display | wwPDB validaton report |
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Full document | 7ubk_full_validation.pdf.gz | 455.4 KB | Display | |
Data in XML | 7ubk_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 7ubk_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/7ubk ftp://data.pdbj.org/pub/pdb/validation_reports/ub/7ubk | HTTPS FTP |
-Related structure data
Related structure data | 7ubjC 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
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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