Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B1C1D1E1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 444.11 kDa 
• Atom Count: 22,900 
• Modelled Residue Count: 3,712 
• Deposited Residue Count: 3,975 
• Unique protein chains: 5

 5BYH

Crystal Structure of Escherichia coli RNA polymerase - Sigma54 Holoenzyme complex

• PDB DOI: 10.2210/pdb5BYH/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12, Klebsiella pneumoniae
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2015-06-10 Released: 2015-09-02 
• Deposition Author(s): Zhang, X., Buck, M., Darbari, V.C., Yang, Y., Zhang, N., Lu, D., Glyde, R., Wang, Y., Winkelman, J., Gourse, R.L., Murakami, K.S.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council, National Institutes of Health, 973 National Key Basic Research Programme

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.76 Å
• R-Value Free: 0.353 
• R-Value Work: 0.346 
• R-Value Observed: 0.347 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 5UI8

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, 5EZK, 5NWT


• 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 K-12	Mutation(s): 0  Gene Names: rpoA, FAZ83_23195, pez, phs, sez, b3295, JW3257 EC: 2.7.7.6
UniProt
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	1,342	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 EC: 2.7.7.6
UniProt
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	1,407	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpoC, tabB, b3988, JW3951 EC: 2.7.7.6
UniProt
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 K-12	Mutation(s): 0  Gene Names: rpoZ, b3649, JW3624 EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12)) Explore P0A800  Go to UniProtKB:  P0A800

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma-54 factor	F [auth M]	477	Klebsiella pneumoniae	Mutation(s): 0  Gene Names:  rpoN, AM386_06570, AM447_14830, B4U21_26550, B4U61_10775, B5L96_24890, BANRA_01956, BANRA_03272, BL124_00020515, BN49_0508, BVX91_19500, C3F39_17700, C4Y50_018355, CK508_022735, DD581_18145, DD583_08830, DM059_27505, DM060_25975, DM062_31185, EAO17_11045, EPB11_01460, FXN67_08250, G5637_17550, G7Z27_02650, GF489_02505, GJI97_002620, GJI97_00400, GJJ08_002620, GJJ08_00400, GNE24_14685, GNG14_08115, GQY16_02610, HJW74_02545, NCTC13465_03419, NCTC1936_05187, NCTC3279_03959, NCTC5047_03164, SAMEA24002668_02395, SAMEA3499901_03507, SAMEA3515094_02864, SAMEA3538546_01627, SAMEA3538560_01627, SAMEA3649435_03395, SAMEA3649466_03329, SAMEA3649630_02927, SAMEA3649650_00080, SAMEA3649733_03935, SAMEA3649758_00080, SAMEA3673026_02122, SAMEA3673122_02180, SAMEA3720909_03353, SAMEA3721038_02488, SAMEA3727579_03145, SAMEA3727651_01748, SAMEA3727679_00080, SAMEA4364603_00630, SAMEA4370540_02816, SAMEA4370542_01833, SAMEA4873581_03318, WP4S18C04_05100
UniProt
Find proteins for R4YEY9 (Klebsiella pneumoniae subsp. rhinoscleromatis SB3432) Explore R4YEY9  Go to UniProtKB:  R4YEY9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	F [auth M]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.76 Å
• R-Value Free: 0.353 
• R-Value Work: 0.346 
• R-Value Observed: 0.347 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 208.48	α = 90
b = 151.52	β = 90
c = 195.28	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-09-02 
Deposition Author(s): Zhang, X., Buck, M., Darbari, V.C., Yang, Y., Zhang, N., Lu, D., Glyde, R., Wang, Y., Winkelman, J., Gourse, R.L., Murakami, K.S.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/H012249/1
National Institutes of Health	United States	GM087350
973 National Key Basic Research Programme	China	2015CB755700

Revision History  

• Version 1.0: 2015-09-02
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Author supporting evidence
• Version 2.0: 2021-06-30
  Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary