6P18

Q21 transcription antitermination complex: loading complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.USA 116: 18384-18390

  • DOI: 10.1073/pnas.1909801116
  • Primary Citation of Related Structures:  

  • 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 promot ...

    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

    Waksman Institute, Rutgers University, Piscataway, NJ 08854; ebright@waksman.rutgers.edu.,Waksman Institute, Rutgers University, Piscataway, NJ 08854.,Rutgers New Jersey Cryo-EM/ET Core Facility, Rutgers University, Piscataway, NJ 08854.,Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ 08854.,Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
A, B
329Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoA (pez, phs, sez)
EC: 2.7.7.6
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Z4
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
C
1342Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoB (groN, nitB, rif, ron, stl, stv, tabD)
EC: 2.7.7.6
Find proteins for P0A8V2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8V2
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
D
1430Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoC (tabB)
EC: 2.7.7.6
Find proteins for P0A8T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8T7
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
E
91Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for P0A800 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A800
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor RpoD
F
627Escherichia coli (strain K12)Mutation(s): 2 
Gene Names: rpoD (alt)
Find proteins for P00579 (Escherichia coli (strain K12))
Go to UniProtKB:  P00579
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Q protein
P, Q
162Phage 21Mutation(s): 0 
Gene Names: Q
Find proteins for Q9XJQ6 (Phage 21)
Go to UniProtKB:  Q9XJQ6
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (67-MER) fragment carrying phage-21 pR' promoter and pause element, nontemplate strand167Phage 21
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (67-MER) fragment carrying phage-21 pR' promoter and pause element, template strand267Phage 21
Entity ID: 9
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*GP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')R11Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement
phenix.real_space_refinerefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 SciencesUnited StatesGM041376

Revision History 

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-09-11
    Type: Data collection, Database references
  • Version 1.2: 2019-09-25
    Type: Data collection, Database references