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 
  • R-Value Observed: 0.265 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Re-refinement Note

This entry reflects an alternative modeling of the original data in:5BYH


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:  
    5UI5, 5UI8

  • PubMed Abstract: 

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

    The bacterial σ factors confer promoter specificity to the RNA polymerase (RNAP). One alternative σ factor, σ N , 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 σ N fragment in complex with its cognate promoter DNA, revealing the molecular details of promoter recognition by σ N The structure allowed us to build and refine an improved σ N -holoenzyme model based on previously published 3.8-Å resolution X-ray data. The improved σ N -holoenzyme model reveals a conserved interdomain interface within σ N 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 σ N in blocking transcription activity and in maintaining the activator sensitivity of σ N .

    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; darst@rockefeller.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaG, H329Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoA, Z4665, ECs4160
EC: 2.7.7.6
Find proteins for P0A7Z6 (Escherichia coli O157:H7)
Explore P0A7Z6 
Go to UniProtKB:  P0A7Z6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaI1342Escherichia coli S88Mutation(s): 0 
Gene Names: rpoB, ECS88_4448
EC: 2.7.7.6
Find proteins for B7MIX3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Explore B7MIX3 
Go to UniProtKB:  B7MIX3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'J1407Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoC, Z5561, ECs4911
EC: 2.7.7.6
Find proteins for P0A8T8 (Escherichia coli O157:H7)
Explore P0A8T8 
Go to UniProtKB:  P0A8T8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaK91Escherichia coli S88Mutation(s): 0 
Gene Names: rpoZ, ECS88_4064
EC: 2.7.7.6
Find proteins for B7MFL0 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Explore B7MFL0 
Go to UniProtKB:  B7MFL0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma-54 factorM477Klebsiella pneumoniaeMutation(s): 0 
Gene Names: SAMEA2273624_03286, SM87_03359, SAMEA104567903_01915, SAMEA104567914_03846
Find proteins for A0A0J4U551 (Klebsiella pneumoniae)
Explore A0A0J4U551 
Go to UniProtKB:  A0A0J4U551
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
J
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates 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 
  • R-Value Observed: 0.265 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.476α = 90
b = 151.524β = 90
c = 195.279γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1 R35 GM118130

Revision History 

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-03-08
    Changes: Data collection, Database references
  • Version 1.2: 2017-03-22
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.4: 2020-01-01
    Changes: Author supporting evidence