4LK0

Crystal Structure Analysis of the E.coli holoenzyme/T7 Gp2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.91 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

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Literature

Phage T7 Gp2 inhibition of Escherichia coli RNA polymerase involves misappropriation of sigma 70 domain 1.1.

Bae, B.Davis, E.Brown, D.Campbell, E.A.Wigneshweraraj, S.Darst, S.A.

(2013) Proc Natl Acad Sci U S A 110: 19772-19777

  • DOI: 10.1073/pnas.1314576110
  • Primary Citation of Related Structures:  
    4LK0, 4LK1, 4LJZ, 4LLG

  • PubMed Abstract: 
  • Bacteriophage T7 encodes an essential inhibitor of the Escherichia coli host RNA polymerase (RNAP), the product of gene 2 (Gp2). We determined a series of X-ray crystal structures of E. coli RNAP holoenzyme with or without Gp2. The results define the structure and location of the RNAP σ(70) subunit domain 1 ...

    Bacteriophage T7 encodes an essential inhibitor of the Escherichia coli host RNA polymerase (RNAP), the product of gene 2 (Gp2). We determined a series of X-ray crystal structures of E. coli RNAP holoenzyme with or without Gp2. The results define the structure and location of the RNAP σ(70) subunit domain 1.1(σ(1.1)(70)) inside the RNAP active site channel, where it must be displaced by the DNA upon formation of the open promoter complex. The structures and associated data, combined with previous results, allow for a complete delineation of the mechanism for Gp2 inhibition of E. coli RNAP. In the primary inhibition mechanism, Gp2 forms a protein-protein interaction with σ(1.1)(70), preventing the normal egress of σ(1.1)(70) from the RNAP active site channel. Gp2 thus misappropriates a domain of the RNAP holoenzyme, σ(1.1)(70), to inhibit the function of the enzyme.


    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha ABGH239Escherichia coli DH1Mutation(s): 0 
Gene Names: rpoAEcDH1_0418ECDH1ME8569_3173
EC: 2.7.7.6
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta CI1342Escherichia coli DH1Mutation(s): 0 
Gene Names: rpoBEcDH1_4008ECDH1ME8569_3846
EC: 2.7.7.6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta' DJ1407Escherichia coli BW2952Mutation(s): 0 
Gene Names: rpoCBWG_3647
EC: 2.7.7.6
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega EK91Escherichia coli DH1Mutation(s): 0 
Gene Names: rpoZEcDH1_0056ECDH1ME8569_3534
EC: 2.7.7.6
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoD FL522Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoDaltb3067JW3039
Find proteins for P00579 (Escherichia coli (strain K12))
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Go to UniProtKB:  P00579
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Bacterial RNA polymerase inhibitor MN64Escherichia phage T7Mutation(s): 0 
Gene Names: 2
Find proteins for P03704 (Escherichia phage T7)
Explore P03704 
Go to UniProtKB:  P03704
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.91 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 186.364α = 90
b = 206.283β = 90
c = 307.999γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
CBASSdata collection

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2013-07-05 
  • Released Date: 2013-11-13 
  • Deposition Author(s): Bae, B., Darst, S.A.

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-13
    Type: Initial release
  • Version 1.1: 2013-12-04
    Changes: Database references
  • Version 1.2: 2013-12-18
    Changes: Database references