3UGP | pdb_00003ugp

Crystal structure of RNA-polymerase sigma subunit domain 2 complexed with -10 promoter element ssDNA oligo (TATAAT)

• PDB DOI: https://doi.org/10.2210/pdb3UGP/pdb
• NAKB: 3UGP

• Classification: TRANSCRIPTION/DNA
• Organism(s): Thermus aquaticus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-11-02 Released: 2011-12-07 
• Deposition Author(s): Feklistov, A., Darst, S.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.238 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Structural basis for promoter-10 element recognition by the bacterial RNA polymerase sigma subunit.

Feklistov, A., Darst, S.A.

(2011) Cell 147: 1257-1269

• PubMed: 22136875 
• DOI: https://doi.org/10.1016/j.cell.2011.10.041
• Primary Citation Related Structures: 
  3UGO, 3UGP


• PubMed Abstract: 
  

  The key step in bacterial promoter opening is recognition of the -10 promoter element (T(-12)A(-11)T(-10)A(-9)A(-8)T(-7) consensus sequence) by the RNA polymerase σ subunit. We determined crystal structures of σ domain 2 bound to single-stranded DNA bearing-10 element sequences. Extensive interactions occur between the protein and the DNA backbone of every -10 element nucleotide. Base-specific interactions occur primarily with A(-11) and T(-7), which are flipped out of the single-stranded DNA base stack and buried deep in protein pockets. The structures, along with biochemical data, support a model where the recognition of the -10 element sequence drives initial promoter opening as the bases of the nontemplate strand are extruded from the DNA double-helix and captured by σ. These results provide a detailed structural basis for the critical roles of A(-11) and T(-7) in promoter melting and reveal important insights into the initiation of transcription bubble formation.

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Organizational Affiliation: 
• The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.09 kDa 
• Atom Count: 1,837 
• Modeled Residue Count: 194 
• Deposited Residue Count: 267 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma factor	A	245	Thermus aquaticus	Mutation(s): 0
UniProt
Find proteins for Q9EZJ8 (Thermus aquaticus) Explore Q9EZJ8  Go to UniProtKB:  Q9EZJ8

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*GP*TP*AP*TP*AP*AP*TP*GP*GP*G)-3'	B, C	11	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	D [auth B], E [auth B], F [auth B], G [auth C], H [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.238 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.001	α = 90
b = 86.001	β = 90
c = 105.862	γ = 90

Software Package:

Software Name	Purpose
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-07 
Deposition Author(s): Feklistov, A., Darst, S.A.

Revision History  

• Version 1.0: 2011-12-07
  Type: Initial release
  
• Version 1.1: 2012-03-07
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description