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 1.5 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: https://doi.org/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 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 .


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaA [auth G],
B [auth H]
329Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoAZ4665ECs4160
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
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UniProt GroupP0A7Z4
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC [auth I]1,342Escherichia coli S88Mutation(s): 0 
Gene Names: rpoBECS88_4448
EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12))
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UniProt GroupP0A8V2
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D [auth J]1,407Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoCZ5561ECs4911
EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE [auth K]91Escherichia coli S88Mutation(s): 0 
Gene Names: rpoZECS88_4064
EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase sigma-54 factorF [auth M]477Klebsiella pneumoniaeMutation(s): 0 
Gene Names: SAMEA2273624_03286SM87_03359
UniProt
Find proteins for A0A0H3H3L1 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286))
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UniProt GroupA0A0H3H3L1
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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

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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  (Full details and data files)

  • 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
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Refinement description