Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - ABCDE Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer -A2BCD 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 389554.56 
• Atom Count: 15410 
• Residue Count: 3498 
• 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 (strain K12)
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG', Escherichia coli


• 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: 8.5 Å
• R-Value Free: 0.470 
• R-Value Work: 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:  
  5NWT, 5BYH
• 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 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. State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, China.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase subunit alpha	A, B	329	Escherichia 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
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase subunit beta	C	1342	Escherichia 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
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase subunit beta'	D	1407	Escherichia 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
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase subunit omega	E	91	Escherichia 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 8.5 Å
• R-Value Free: 0.470 
• R-Value Work: 0.470 
• Space Group: P 6₃

Unit Cell:

Length (Å)	Angle (°)
a = 255.544	α = 90.00
b = 255.544	β = 90.00
c = 189.392	γ = 120.00

Software Package:

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

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
  Type: Author supporting evidence