5NWT

Crystal Structure of Escherichia coli RNA polymerase - Sigma54 Holoenzyme complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.76 Å
  • R-Value Free: 0.370 
  • R-Value Work: 0.313 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

TRANSCRIPTION. Structures of the RNA polymerase-Sigma54 reveal new and conserved regulatory strategies.

Yang, Y.Darbari, V.C.Zhang, N.Lu, D.Glyde, R.Wang, Y.P.Winkelman, J.T.Gourse, R.L.Murakami, K.S.Buck, M.Zhang, X.

(2015) Science 349: 882-885

  • DOI: 10.1126/science.aab1478
  • Primary Citation of Related Structures:  
  • Also Cited By: 5UI8

  • PubMed Abstract: 
  • Transcription by RNA polymerase (RNAP) in bacteria requires specific promoter recognition by σ factors. The major variant σ factor (σ(54)) initially forms a transcriptionally silent complex requiring specialized adenosine triphosphate-dependent activ ...

    Transcription by RNA polymerase (RNAP) in bacteria requires specific promoter recognition by σ factors. The major variant σ factor (σ(54)) initially forms a transcriptionally silent complex requiring specialized adenosine triphosphate-dependent activators for initiation. Our crystal structure of the 450-kilodalton RNAP-σ(54) holoenzyme at 3.8 angstroms reveals molecular details of σ(54) and its interactions with RNAP. The structure explains how σ(54) targets different regions in RNAP to exert its inhibitory function. Although σ(54) and the major σ factor, σ(70), have similar functional domains and contact similar regions of RNAP, unanticipated differences are observed in their domain arrangement and interactions with RNAP, explaining their distinct properties. Furthermore, we observe evolutionarily conserved regulatory hotspots in RNAPs that can be targeted by a diverse range of mechanisms to fine tune transcription.


    Organizational Affiliation

    Centre for Structural Biology, Imperial College London, South Kensington SW7 2AZ, UK. State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, China.,Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.,State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, China.,Centre for Structural Biology, Imperial College London, South Kensington SW7 2AZ, UK. Department of Medicine, Imperial College London, South Kensington SW7 2AZ, UK.,Department of Life Sciences, Imperial College London, South Kensington SW7 2AZ, UK.,Centre for Structural Biology, Imperial College London, South Kensington SW7 2AZ, UK. Department of Medicine, Imperial College London, South Kensington SW7 2AZ, UK. xiaodong.zhang@imperial.ac.uk.,Centre for Structural Biology, Imperial College London, South Kensington SW7 2AZ, UK.,Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA.




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-54 factor,RNA polymerase sigma-54 factor
M
477Klebsiella pneumoniae subsp. rhinoscleromatis SB3432Mutation(s): 0 
Gene Names: rpoN
Find proteins for R4YEY9 (Klebsiella pneumoniae subsp. rhinoscleromatis SB3432)
Go to UniProtKB:  R4YEY9
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
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
M
L-PEPTIDE LINKINGC4 H9 N O2

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MSE
Query on MSE
M
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.76 Å
  • R-Value Free: 0.370 
  • R-Value Work: 0.313 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 208.477α = 90.00
b = 151.525β = 90.00
c = 195.279γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release