5UI8

structure of sigmaN-holoenzyme

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.76 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.262 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 5BYH - determined by Zhang, X., Buck, M., Darbari, V.C., Yang, Y., Zhang, N., Lu, D., Glyde, R., Wang, Y., Winkelman, J., Gourse, R.L., Murakami, K.S.  

Literature

Crystal structure of Aquifex aeolicus sigma (N) bound to promoter DNA and the structure of sigma (N)-holoenzyme.

Campbell, E.A., Kamath, S., Rajashankar, K.R., Wu, M., Darst, S.A.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: E1805-E1814

  • DOI: 10.1073/pnas.1619464114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The bacterial σ factors confer promoter specificity to the RNA polymerase (RNAP). One alternative σ factor, σN, is unique in its structure and functional mechanism, forming transcriptionally inactive promoter complexes that require activation by spec ...

    The bacterial σ factors confer promoter specificity to the RNA polymerase (RNAP). One alternative σ factor, σN, is unique in its structure and functional mechanism, forming transcriptionally inactive promoter complexes that require activation by specialized AAA+ ATPases. We report a 3.4-Å resolution X-ray crystal structure of a σN fragment in complex with its cognate promoter DNA, revealing the molecular details of promoter recognition by σN The structure allowed us to build and refine an improved σN-holoenzyme model based on previously published 3.8-Å resolution X-ray data. The improved σN-holoenzyme model reveals a conserved interdomain interface within σN that, when disrupted by mutations, leads to transcription activity without activator intervention (so-called bypass mutants). Thus, the structure and stability of this interdomain interface are crucial for the role of σN in blocking transcription activity and in maintaining the activator sensitivity of σN.

    Related Citations: 
    • TRANSCRIPTION. Structures of the RNA polymerase-sigma 54 reveal new and conserved regulatory strategies.
      Yang, Y.,Darbari, V.C.,Zhang, N.,Lu, D.,Glyde, R.,Wang, Y.P.,Winkelman, J.T.,Gourse, R.L.,Murakami, K.S.,Buck, M.,Zhang, X.
      (2015) Science 349: 882

    Organizational Affiliation: 

    Laboratory for Molecular Biophysics, The Rockefeller University, New York, NY 10065.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
G, H
329Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
Find proteins for P0A7Z6 (Escherichia coli O157:H7)
Go to UniProtKB:  P0A7Z6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
I
1342Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
Find proteins for B7MIX3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MIX3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
J
1407Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoC
EC: 2.7.7.6
Find proteins for P0A8T8 (Escherichia coli O157:H7)
Go to UniProtKB:  P0A8T8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
K
91Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for B7MFL0 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MFL0
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma-54 factor
M
477Klebsiella pneumoniaeMutation(s): 0 
Gene Names: rpoN
Find proteins for A0A0J4U551 (Klebsiella pneumoniae)
Go to UniProtKB:  A0A0J4U551
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
J
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
J
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.76 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.262 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 208.476α = 90.00
b = 151.524β = 90.00
c = 195.279γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States1 R35 GM118130

Revision History 

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-03-08
    Type: Data collection, Database references
  • Version 1.2: 2017-03-22
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence