1KU7

Crystal Structure of Thermus aquatics RNA Polymerase SigmaA Subunit Region 4 Bound to-35 Element DNA

• PDB DOI: https://doi.org/10.2210/pdb1KU7/pdb
• NAKB: 1KU7

• Classification: TRANSCRIPTION/DNA
• Organism(s): Thermus aquaticus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-01-21 Released: 2002-03-29 
• Deposition Author(s): Campbell, E.A., Muzzin, O., Chlenov, M., Sun, J.L., Olson, C.A., Weinman, O., Trester-Zedlitz, M.L., Darst, S.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.293 
• R-Value Work: 0.255 
• R-Value Observed: 0.255 

Literature

Structure of the bacterial RNA polymerase promoter specificity sigma subunit.

Campbell, E.A., Muzzin, O., Chlenov, M., Sun, J.L., Olson, C.A., Weinman, O., Trester-Zedlitz, M.L., Darst, S.A.

(2002) Mol Cell 9: 527-539

• PubMed: 11931761 
• DOI: https://doi.org/10.1016/s1097-2765(02)00470-7
• Primary Citation of Related Structures:  
  1KU2, 1KU3, 1KU7


• PubMed Abstract: 
  

  The sigma subunit is the key regulator of bacterial transcription. Proteolysis of Thermus aquaticus sigma(A), which occurred in situ during crystallization, reveals three domains, sigma(2), sigma(3), and sigma(4), connected by flexible linkers. Crystal structures of each domain were determined, as well as of sigma(4) complexed with -35 element DNA. Exposed surfaces of each domain are important for RNA polymerase binding. Universally conserved residues important for -10 element recognition and melting lie on one face of sigma(2), while residues important for extended -10 recognition lie on sigma(3). Genetic studies correctly predicted that a helix-turn-helix motif in sigma(4) recognizes the -35 element but not the details of the protein-DNA interactions. Positive control mutants in sigma(4) cluster in two regions, positioned to interact with activators bound just upstream or downstream of the -35 element.

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Organizational Affiliation: 

Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24.14 kDa 
• Atom Count: 1,645 
• Modelled Residue Count: 163 
• Deposited Residue Count: 168 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
sigma factor sigA	C [auth A], D	73	Thermus aquaticus	Mutation(s): 1
UniProt
Find proteins for Q9EZJ8 (Thermus aquaticus) Explore Q9EZJ8  Go to UniProtKB:  Q9EZJ8

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*CP*TP*TP*GP*AP*CP*AP*AP*AP*G)-3'	A [auth B]	11	N/A

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.293 
• R-Value Work: 0.255 
• R-Value Observed: 0.255 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.18	α = 90
b = 62.65	β = 90
c = 94.81	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-03-29 
Deposition Author(s): Campbell, E.A., Muzzin, O., Chlenov, M., Sun, J.L., Olson, C.A., Weinman, O., Trester-Zedlitz, M.L., Darst, S.A.

Revision History  

• Version 1.0: 2002-03-29
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references
• Version 1.4: 2024-02-14
  Changes: Data collection