4KI2

Crystallographic analysis of an RNA-polymerase sigma-subunit fragment complexed with -10 promoter element ssDNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic analysis of an RNA polymerase sigma-subunit fragment complexed with -10 promoter element ssDNA: quadruplex formation as a possible tool for engineering crystal contacts in protein-ssDNA complexes.

Feklistov, A.Darst, S.A.

(2013) Acta Crystallogr.,Sect.F 69: 950-955

  • DOI: 10.1107/S1744309113020368

  • PubMed Abstract: 
  • Structural studies of -10 promoter element recognition by domain 2 of the RNA polymerase σ subunit [Feklistov & Darst (2011), Cell, 147, 1257-1269] reveal an unusual crystal-packing arrangement dominated by G-quartets. The 3'-terminal GGG motif of th ...

    Structural studies of -10 promoter element recognition by domain 2 of the RNA polymerase σ subunit [Feklistov & Darst (2011), Cell, 147, 1257-1269] reveal an unusual crystal-packing arrangement dominated by G-quartets. The 3'-terminal GGG motif of the oligonucleotide used in crystallization participates in G-quadruplex formation with GGG motifs from symmetry-related complexes. Stacking between neighboring G-quadruplexes results in the formation of pseudo-continuous four-stranded columns running throughout the length of the crystal (G-columns). Here, a new crystal form is presented with a different arrangement of G-columns and it is proposed that the fortuitous finding of G-quartet packing could be useful in engineering crystal contacts in protein-ssDNA complexes.


    Organizational Affiliation

    Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA. afeklistov@rockefeller.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor
A, B
245Thermus aquaticusGene Names: sigA
Find proteins for Q9EZJ8 (Thermus aquaticus)
Go to UniProtKB:  Q9EZJ8
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3')D,E,F,G11N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
D, G
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.212 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 118.110α = 90.00
b = 118.110β = 90.00
c = 200.845γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
CBASSdata collection
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-04
    Type: Initial release
  • Version 1.1: 2014-09-24
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Structure summary