Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 389.55 kDa 
• Atom Count: 15410 
• Residue Count: 3129 
• Unique protein chains: 4

5EZK

RNA polymerase model placed by Molecular replacement into X-ray diffraction map of DNA-bound RNA Polymerase-Sigma 54 holoenzyme complex.

• DOI: 10.2210/pdb5EZK/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG, Escherichia coli
• Mutation(s): No 


• Deposited: 2015-11-26 Released: 2015-12-16 
• Deposition Author(s): Darbari, V.C., Yang, Y., Lu, D., Zhang, N., Glyde, R., Wang, Y., Murakami, K.S., Buck, M., Zhang, X.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 8.50 Å
• R-Value Free: 0.470 
• R-Value Work: 0.470 
• R-Value Observed: 0.470 

Literature

TRANSCRIPTION. Structures of the RNA polymerase- Sigma 54 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

• PubMed: 26293966 
• DOI: 10.1126/science.aab1478
• Primary Citation of Related Structures:  
  5BYH, 5NWT, 5EZK


• 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 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.

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Organizational Affiliation: 

Centre for Structural Biology, Imperial College London, South Kensington SW7 2AZ, UK. Department of Medicine, Imperial College London, South Kensington SW7 2AZ, UK. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	A, B	329	Escherichia coli	Mutation(s): 0  Gene Names: rpoA, Z4665, ECs4160 EC: 2.7.7.6
Find proteins for P0A7Z4 (Escherichia coli (strain K12)) Explore P0A7Z4  Go to UniProtKB:  P0A7Z4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	C	1342	Escherichia coli	Mutation(s): 0  Gene Names: rpoB, Z5560, ECs4910 EC: 2.7.7.6
Find proteins for P0A8V2 (Escherichia coli (strain K12)) Explore P0A8V2  Go to UniProtKB:  P0A8V2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	D	1407	Escherichia coli	Mutation(s): 0  Gene Names: rpoC, Z5561, ECs4911 EC: 2.7.7.6
Find proteins for P0A8T7 (Escherichia coli (strain K12)) Explore P0A8T7  Go to UniProtKB:  P0A8T7

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	E	91	Escherichia coli	Mutation(s): 0  Gene Names: rpoZ, b3649, JW3624 EC: 2.7.7.6
Find proteins for P0A800 (Escherichia coli (strain K12)) Explore P0A800  Go to UniProtKB:  P0A800

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 8.50 Å
• R-Value Free: 0.470 
• R-Value Work: 0.470 
• R-Value Observed: 0.470 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 255.544	α = 90
b = 255.544	β = 90
c = 189.392	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-11-26 
• Released Date: 2015-12-16 
Deposition Author(s): Darbari, V.C., Yang, Y., Lu, D., Zhang, N., Glyde, R., Wang, Y., Murakami, K.S., Buck, M., Zhang, X.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	--

Revision History 

• Version 1.0: 2015-12-16
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Author supporting evidence