4YG2

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
A, B, G, H
329Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
Find proteins for P0A7Z6 (Escherichia coli O157:H7)
Go to UniProtKB:  P0A7Z6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
C, I
1342Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
Find proteins for P0A8V4 (Escherichia coli O157:H7)
Go to UniProtKB:  P0A8V4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
D, J
1407Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoC
EC: 2.7.7.6
Find proteins for P0A8T8 (Escherichia coli O157:H7)
Go to UniProtKB:  P0A8T8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
E, K
91Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for P0A802 (Escherichia coli O157:H7)
Go to UniProtKB:  P0A802
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
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 
C, D, I, J
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 187.308α = 90.00
b = 205.901β = 90.00
c = 309.185γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
Cootmodel building
PHENIXrefinement

Structure Validation

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View more in-depth experimental data

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 SciencesUnited StatesGM087350

Revision History 

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