6P1A

Transcription antitermination factor Q21 in complex with Q21-binding-element DNA

  • Classification: GENE REGULATION
  • Organism(s): Phage 21
  • Expression System: Escherichia coli BL21
  • Mutation(s): No 

  • Deposited: 2019-05-19 Released: 2019-06-26 
  • Deposition Author(s): Yin, Z., Ebright, R.H.
  • Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of Q-dependent antitermination.

Yin, Z.Kaelber, J.T.Ebright, R.H.

(2019) Proc Natl Acad Sci U S A 116: 18384-18390

  • DOI: 10.1073/pnas.1909801116
  • Primary Citation of Related Structures:  
    6P18, 6P19, 6P1A, 6P1B, 6P1C

  • PubMed Abstract: 
  • Lambdoid bacteriophage Q protein mediates the switch from middle to late bacteriophage gene expression by enabling RNA polymerase (RNAP) to read through transcription terminators preceding bacteriophage late genes. Q loads onto RNAP engaged in promoter-proximal pausing at a Q binding element (QBE) and adjacent sigma-dependent pause element (SDPE) to yield a Q-loading complex, and Q subsequently translocates with RNAP as a pausing-deficient, termination-deficient Q-loaded complex ...

    Lambdoid bacteriophage Q protein mediates the switch from middle to late bacteriophage gene expression by enabling RNA polymerase (RNAP) to read through transcription terminators preceding bacteriophage late genes. Q loads onto RNAP engaged in promoter-proximal pausing at a Q binding element (QBE) and adjacent sigma-dependent pause element (SDPE) to yield a Q-loading complex, and Q subsequently translocates with RNAP as a pausing-deficient, termination-deficient Q-loaded complex. Here, we report high-resolution structures of 4 states on the pathway of antitermination by Q from bacteriophage 21 (Q21): Q21, the Q21-QBE complex, the Q21-loading complex, and the Q21-loaded complex. The results show that Q21 forms a torus, a "nozzle," that narrows and extends the RNAP RNA-exit channel, extruding topologically linked single-stranded RNA and preventing the formation of pause and terminator hairpins.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Q proteinA, B, C162Phage 21Mutation(s): 0 
Gene Names: Q
UniProt
Find proteins for Q9XJQ6 (Phage 21)
Explore Q9XJQ6 
Go to UniProtKB:  Q9XJQ6
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*CP*TP*CP*AP*TP*TP*GP*AP*GP*CP*AP*AP*AP*TP*GP*AP*GP*CP*AP*AP*G)-3')D, F21Phage 21
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*TP*TP*GP*CP*TP*CP*AP*TP*TP*TP*GP*CP*TP*CP*AP*AP*TP*GP*AP*G)-3')E, G21Phage 21
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.235 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.573α = 90
b = 263.224β = 90
c = 56.77γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-05-19 
  • Released Date: 2019-06-26 
  • Deposition Author(s): Yin, Z., Ebright, R.H.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesGM041376

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-09-11
    Changes: Data collection, Database references
  • Version 1.2: 2019-09-25
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence