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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaGH329Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoAZ4665ECs4160
EC: 2.7.7.6
Find proteins for P0A7Z6 (Escherichia coli O157:H7)
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Go to UniProtKB:  P0A7Z6
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaI1342Escherichia coli S88Mutation(s): 0 
Gene Names: rpoBECS88_4448
EC: 2.7.7.6
Find proteins for B7MIX3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'J1407Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoCZ5561ECs4911
EC: 2.7.7.6
Find proteins for P0A8T8 (Escherichia coli O157:H7)
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Go to UniProtKB:  P0A8T8
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaK91Escherichia coli S88Mutation(s): 0 
Gene Names: rpoZECS88_4064
EC: 2.7.7.6
Find proteins for B7MFL0 (Escherichia coli O45:K1 (strain S88 / ExPEC))
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma-54 factorM477Klebsiella pneumoniaeMutation(s): 0 
Gene Names: SAMEA2273624_03286SM87_03359SAMEA104567903_01915SAMEA104567914_03846
Find proteins for A0A0J4U551 (Klebsiella pneumoniae)
Explore A0A0J4U551 
Go to UniProtKB:  A0A0J4U551
Protein Feature View
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  • 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

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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 

  • 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