4YG2

X-ray crystal structur of Escherichia coli RNA polymerase sigma70 holoenzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

X-ray crystal structure of Escherichia coli RNA polymerase sigma70 holoenzyme

Murakami, K.S.

(2013) J Biol Chem 288: 9126-9134

  • DOI: 10.1074/jbc.M112.430900
  • Primary Citation of Related Structures:  
    4YG2

  • PubMed Abstract: 
  • Escherichia coli RNA polymerase (RNAP) is the most studied bacterial RNAP and has been used as the model RNAP for screening and evaluating potential RNAP-targeting antibiotics. However, the x-ray crystal structure of E. coli RNAP has been limited to ...

    Escherichia coli RNA polymerase (RNAP) is the most studied bacterial RNAP and has been used as the model RNAP for screening and evaluating potential RNAP-targeting antibiotics. However, the x-ray crystal structure of E. coli RNAP has been limited to individual domains. Here, I report the x-ray structure of the E. coli RNAP σ(70) holoenzyme, which shows σ region 1.1 (σ1.1) and the α subunit C-terminal domain for the first time in the context of an intact RNAP. σ1.1 is positioned at the RNAP DNA-binding channel and completely blocks DNA entry to the RNAP active site. The structure reveals that σ1.1 contains a basic patch on its surface, which may play an important role in DNA interaction to facilitate open promoter complex formation. The α subunit C-terminal domain is positioned next to σ domain 4 with a fully stretched linker between the N- and C-terminal domains. E. coli RNAP crystals can be prepared from a convenient overexpression system, allowing further structural studies of bacterial RNAP mutants, including functionally deficient and antibiotic-resistant RNAPs.


    Related Citations: 
    • X-ray Crystal Structures of Escherichia coli RNA Polymerase with Switch Region Binding Inhibitors Enable Rational Design of Squaramides with an Improved Fraction Unbound to Human Plasma Protein.
      Molodtsov, V., Fleming, P.R., Eyermann, C.J., Ferguson, A.D., Foulk, M.A., McKinney, D.C., Masse, C.E., Buurman, E.T., Murakami, K.S.
      (2015) J Med Chem 58: 3156

    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA. kum14@psu.edu



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaABGH329Escherichia 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 betaCI1342Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoBZ5560ECs4910
EC: 2.7.7.6
Find proteins for P0A8V4 (Escherichia coli O157:H7)
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Go to UniProtKB:  P0A8V4
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'DJ1407Escherichia 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 omegaEK91Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoZZ5075ECs4524
EC: 2.7.7.6
Find proteins for P0A802 (Escherichia coli O157:H7)
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoDFL613Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoDaltb3067JW3039
Find proteins for P00579 (Escherichia coli (strain K12))
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 187.308α = 90
b = 205.901β = 90
c = 309.185γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-02-25 
  • Released Date: 2015-03-18 
  • Deposition Author(s): Murakami, K.S.
  • This entry supersedes: 4IGC

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM087350

Revision History 

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2015-04-22
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence