6C9Y

Cryo-EM structure of E. coli RNAP sigma70 holoenzyme


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cryo-EM structure ofEscherichia colisigma70RNA polymerase and promoter DNA complex revealed a role of sigma non-conserved region during the open complex formation.

Narayanan, A.Vago, F.S.Li, K.Qayyum, M.Z.Yernool, D.Jiang, W.Murakami, K.S.

(2018) J. Biol. Chem. 293: 7367-7375

  • DOI: 10.1074/jbc.RA118.002161
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • First step of gene expression is transcribing the genetic information stored in DNA to RNA by the transcription machinery including RNA polymerase (RNAP). In <i>Escherichia coli </i>, a primary σ <sup>70 </sup> factor forms the RNAP holoenzyme to ex ...

    First step of gene expression is transcribing the genetic information stored in DNA to RNA by the transcription machinery including RNA polymerase (RNAP). In Escherichia coli , a primary σ 70 factor forms the RNAP holoenzyme to express housekeeping genes. The σ 70 contains a large insertion between the conserved regions 1.2 and 2.1, the σ non-conserved region (σ NCR ), but its function remains to be elucidated. In this study, we determined the cryo-EM structures of the E. coli RNAP σ 70 holoenzyme and its complex with promoter DNA (open complex, RPo) at 4.2 and 5.75 Å resolutions, respectively, to reveal native conformations of RNAP and DNA. The RPo structure presented here found an interaction between the σ NCR and promoter DNA just upstream of the -10 element, which was not observed in a previously determined E. coli RNAP transcription initiation complex (RPo plus short RNA) structure by X-ray crystallography because of restraint of crystal packing effects. Disruption of the σ NCR and DNA interaction by the amino acid substitutions (R157A/R157E) influences the DNA opening around the transcription start site and therefore decreases the transcription activity of RNAP. We propose that the σ NCR and DNA interaction is conserved in proteobacteria, and RNAP in other bacteria replaces its role with a transcription factor.


    Organizational Affiliation

    Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, Indiana 47906.,From the Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802 and kum14@psu.edu.,From the Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802 and.,Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, Indiana 47906 jiang12@purdue.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
A, B
329Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoA (pez, phs, sez)
EC: 2.7.7.6
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Z4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
C
1342Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoB (groN, nitB, rif, ron, stl, stv, tabD)
EC: 2.7.7.6
Find proteins for P0A8V2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8V2
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
D
1407Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoC (tabB)
EC: 2.7.7.6
Find proteins for P0A8T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8T7
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
E
91Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for P0A800 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A800
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor RpoD
F
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
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM087350
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM093142

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-04-11
    Type: Data collection, Database references
  • Version 1.2: 2018-05-23
    Type: Data collection, Database references