4LLG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7936 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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.USA 110: 19772-19777

  • DOI: 10.1073/pnas.1314576110
  • Primary Citation of Related Structures:  

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
A, B, G, H
239N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
C, I
1342N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
D, J
1407N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
E, K
91N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor RpoD
F, L
613Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoD (alt)
Find proteins for P00579 (Escherichia coli (strain K12))
Go to UniProtKB:  P00579
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Bacterial RNA polymerase inhibitor
M, N
64Enterobacteria phage T7Mutation(s): 0 
Find proteins for P03704 (Enterobacteria phage T7)
Go to UniProtKB:  P03704
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
D, J
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
D, J
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7936 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.243 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 187.510α = 90.00
b = 205.038β = 90.00
c = 308.797γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
SCALEPACKdata scaling
HKL-2000data reduction
CBASSdata collection
PHASERphasing
PHENIXrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-07-09 
  • Released Date: 2013-11-13 
  • Deposition Author(s): Bae, B., Darst, S.A.

Revision History 

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