6P1A | pdb_00006p1a

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

• PDB DOI: https://doi.org/10.2210/pdb6P1A/pdb
• NAKB: 6P1A

• Classification: GENE REGULATION
• Organism(s): Escherichia 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 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

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

• PubMed: 31455742 
• DOI: https://doi.org/10.1073/pnas.1909801116
• Primary Citation 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. 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.
Department of Chemistry and Chemical Biology, 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.
Waksman Institute, Rutgers University, Piscataway, NJ 08854; [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 82.03 kDa 
• Atom Count: 5,368 
• Modeled Residue Count: 534 
• Deposited Residue Count: 570 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Q protein	A, B, C	162	Escherichia phage 21	Mutation(s): 0
UniProt
Find proteins for Q9XJQ6 (Escherichia phage 21) Explore Q9XJQ6  Go to UniProtKB:  Q9XJQ6

Entity ID: 2
Molecule	Chains	Length	Organism	Image
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, F	21	Escherichia phage 21

Entity ID: 3
Molecule	Chains	Length	Organism	Image
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, G	21	Escherichia phage 21

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	H [auth A], I [auth A], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	K [auth B], L [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free:  0.275 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.573	α = 90
b = 263.224	β = 90
c = 56.77	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	GM041376

Revision History  

• 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
• Version 1.4: 2023-10-11
  Changes: Data collection, Database references, Refinement description